From 6a0b7bedde11a56d6aa94519e37f3da9ba454608 Mon Sep 17 00:00:00 2001 From: acballesteros Date: Wed, 8 Nov 2023 21:45:23 +0000 Subject: [PATCH] deploy: 15953de79dfc870adaa39cd40ed7de491139806c --- AMBER/Tutorial-8.html | 12 ++++++------ Tutorials amber.html | 12 ++++++------ _sources/AMBER/Tutorial-8.rst.txt | 12 ++++++------ searchindex.js | 2 +- 4 files changed, 19 insertions(+), 19 deletions(-) diff --git a/AMBER/Tutorial-8.html b/AMBER/Tutorial-8.html index bebe25f..a85c7ca 100644 --- a/AMBER/Tutorial-8.html +++ b/AMBER/Tutorial-8.html @@ -104,11 +104,11 @@

8.1. Build CG representationsCaution

The mapping to CG requires the correct protonation state of each residue at a given pH. We recommend using the CHARMM-GUI server with the Glycan Reader & Modeler to prepare your system, choosing the output naming scheme of AMBER for best compatibility. An account is required to access any of the CHARMM-GUI Input Generator modules, and it can take up to 24 hours to obtain one.

-

This example use the structure of glycoprotein 1GYA, using CHARMM-GUI server are obtained the files parm7 and rst7, this files are converted to pdb format with naming scheme of AMBER/GLYCAM using AmberTool as follow:

+

This example use the structure of glycoprotein 1GYA, using CHARMM-GUI server are obtained the files parm7 and rst7, these files are converted to pdb format with the naming scheme of AMBER/GLYCAM using AmberTool as follow:

ambpdb -p ./sirah.amber/tutorial/8/step3_input.parm7 -c ./sirah.amber/tutorial/8/step3_input.rst7 > 1GYA_glycam.pdb
-

From the file 1GYA_glycam.pdb generated delete the solvent, rename to 1GYA_glycam_NoW.pdb and then map the protonated atomistic to its CG representation:

+

From the file 1GYA_glycam.pdb generated delete the solvent, rename to 1GYA_glycam_NoW.pdb and then map the protonated atomistic structure to its CG representation:

./sirah.amber/tools/CGCONV/cgconv.pl -i ./sirah.amber/tutorial/8/1GYA_glycam_NoW.pdb -o 1GYA_cg.pdb
@@ -126,7 +126,7 @@

8.1. Build CG representations

Important

-

By default charged termini are used, but it is possible to set them neutral by renaming the residues from s[code] to a[code] (Nt-acetylated) or m[code] (Ct-amidated) after mapping to CG, where [code] is the root residue name in SIRAH. For example, to set a neutral N-terminal Histidine protonated at epsilon nitrogen (\(N_{\epsilon}\)) rename it from “sHe” to “aHe”.

+

By default, charged termini are used. However, it is possible to set them neutral by renaming the residues from s[code] to a[code] (Nt-acetylated) or m[code] (Ct-amidated) after mapping to CG, where [code] is the root residue name in SIRAH. For example, to set a neutral N-terminal Histidine protonated at epsilon nitrogen (\(N_{\epsilon}\)) rename it from “sHe” to “aHe”.

Please check both PDBs structures using VMD:

vmd -m sirah.amber/tutorial/8/1GYA_glycam_NoW.pdb 1GYA_cg.pdb
@@ -213,7 +213,7 @@ 
8.4. Run the simulation

The folder sirah.amber/tutorial/8/ contains typical input files for energy minimization -(em1_WT4.in and em2_WT4.in), equilibration (eq1_WT4.in and eq2_WT4.in) and production (md_WT4.in) runs. Please check carefully the +(em1_WT4.in and em2_WT4.in), relaxation (or equilibration) (eq1_WT4.in and eq2_WT4.in) and production (md_WT4.in) runs. Please check carefully the input flags therein, in particular the definition of flag chngmask=0 at &ewald section is mandatory.

Tip

@@ -246,7 +246,7 @@

8.4. Run the simulation
pmemd.cuda -O -i ../sirah.amber/tutorial/8/em2_WT4.in -p ../1GYA_cg.prmtop -c ../1GYA_cg_em1.ncrst -o 1GYA_cg_em2.out -r 1GYA_cg_em2.ncrst &

-

Solvent Equilibration (NPT):

+

Solvent Relaxation (or equlibration) in NPT:

pmemd.cuda -O -i ../sirah.amber/tutorial/8/eq1_WT4.in -p ../1GYA_cg.prmtop -c 1GYA_cg_em2.ncrst -ref 1GYA_cg_em2.ncrst -o 1GYA_cg_eq1.out -r 1GYA_cg_eq1.ncrst -x 1GYA_cg_eq1.nc &
@@ -254,7 +254,7 @@

8.4. Run the simulationCaution

Option restraintmask=:’1-114’ in input file eq1_WT4.in must be set specifically for each system to embrace all glycoprotein’s residues.

-

Soft equilibration to improve side chain and glycan solvation (NPT):

+

Soft Relaxation to improve side chain and glycan solvation (NPT):

pmemd.cuda -O -i ../sirah.amber/tutorial/8/eq2_WT4.in -p ../1GYA_cg.prmtop -c 1GYA_cg_eq1.ncrst -ref 1GYA_cg_eq1.ncrst -o 1GYA_cg_eq2.out -r 1GYA_cg_eq2.ncrst -x 1GYA_cg_eq2.nc &
diff --git a/Tutorials amber.html b/Tutorials amber.html index 9dc8fc0..4b329c7 100644 --- a/Tutorials amber.html +++ b/Tutorials amber.html @@ -1555,11 +1555,11 @@

8.1. Build CG representationsCaution

The mapping to CG requires the correct protonation state of each residue at a given pH. We recommend using the CHARMM-GUI server with the Glycan Reader & Modeler to prepare your system, choosing the output naming scheme of AMBER for best compatibility. An account is required to access any of the CHARMM-GUI Input Generator modules, and it can take up to 24 hours to obtain one.

-

This example use the structure of glycoprotein 1GYA, using CHARMM-GUI server are obtained the files parm7 and rst7, this files are converted to pdb format with naming scheme of AMBER/GLYCAM using AmberTool as follow:

+

This example use the structure of glycoprotein 1GYA, using CHARMM-GUI server are obtained the files parm7 and rst7, these files are converted to pdb format with the naming scheme of AMBER/GLYCAM using AmberTool as follow:

ambpdb -p ./sirah.amber/tutorial/8/step3_input.parm7 -c ./sirah.amber/tutorial/8/step3_input.rst7 > 1GYA_glycam.pdb
-

From the file 1GYA_glycam.pdb generated delete the solvent, rename to 1GYA_glycam_NoW.pdb and then map the protonated atomistic to its CG representation:

+

From the file 1GYA_glycam.pdb generated delete the solvent, rename to 1GYA_glycam_NoW.pdb and then map the protonated atomistic structure to its CG representation:

./sirah.amber/tools/CGCONV/cgconv.pl -i ./sirah.amber/tutorial/8/1GYA_glycam_NoW.pdb -o 1GYA_cg.pdb
@@ -1577,7 +1577,7 @@

8.1. Build CG representations

Important

-

By default charged termini are used, but it is possible to set them neutral by renaming the residues from s[code] to a[code] (Nt-acetylated) or m[code] (Ct-amidated) after mapping to CG, where [code] is the root residue name in SIRAH. For example, to set a neutral N-terminal Histidine protonated at epsilon nitrogen (\(N_{\epsilon}\)) rename it from “sHe” to “aHe”.

+

By default, charged termini are used. However, it is possible to set them neutral by renaming the residues from s[code] to a[code] (Nt-acetylated) or m[code] (Ct-amidated) after mapping to CG, where [code] is the root residue name in SIRAH. For example, to set a neutral N-terminal Histidine protonated at epsilon nitrogen (\(N_{\epsilon}\)) rename it from “sHe” to “aHe”.

Please check both PDBs structures using VMD:

vmd -m sirah.amber/tutorial/8/1GYA_glycam_NoW.pdb 1GYA_cg.pdb
@@ -1664,7 +1664,7 @@ 
8.4. Run the simulationsirah.amber/tutorial/8/ contains typical input files for energy minimization
-(em1_WT4.in and em2_WT4.in), equilibration (eq1_WT4.in and eq2_WT4.in) and production (md_WT4.in) runs. Please check carefully the
+(em1_WT4.in and em2_WT4.in), relaxation (or equilibration) (eq1_WT4.in and eq2_WT4.in) and production (md_WT4.in) runs. Please check carefully the
 input flags therein, in particular the definition of flag chngmask=0 at &ewald section is mandatory.

 

 
Tip

@@ -1697,7 +1697,7 @@ 
8.4. Run the simulation
pmemd.cuda -O -i ../sirah.amber/tutorial/8/em2_WT4.in -p ../1GYA_cg.prmtop -c ../1GYA_cg_em1.ncrst -o 1GYA_cg_em2.out -r 1GYA_cg_em2.ncrst &
 

 

-
Solvent Equilibration (NPT):

+
Solvent Relaxation (or equlibration) in NPT:

 
pmemd.cuda -O -i ../sirah.amber/tutorial/8/eq1_WT4.in -p ../1GYA_cg.prmtop -c 1GYA_cg_em2.ncrst -ref 1GYA_cg_em2.ncrst -o 1GYA_cg_eq1.out -r 1GYA_cg_eq1.ncrst -x 1GYA_cg_eq1.nc &
 

 

@@ -1705,7 +1705,7 @@ 
8.4. Run the simulationCaution

 
Option restraintmask=:’1-114’ in input file eq1_WT4.in must be set specifically for each system to embrace all glycoprotein’s residues.
-

Soft equilibration to improve side chain and glycan solvation (NPT):

+

Soft Relaxation to improve side chain and glycan solvation (NPT):

pmemd.cuda -O -i ../sirah.amber/tutorial/8/eq2_WT4.in -p ../1GYA_cg.prmtop -c 1GYA_cg_eq1.ncrst -ref 1GYA_cg_eq1.ncrst -o 1GYA_cg_eq2.out -r 1GYA_cg_eq2.ncrst -x 1GYA_cg_eq2.nc &
diff --git a/_sources/AMBER/Tutorial-8.rst.txt b/_sources/AMBER/Tutorial-8.rst.txt index 156a998..a457e1d 100644 --- a/_sources/AMBER/Tutorial-8.rst.txt +++ b/_sources/AMBER/Tutorial-8.rst.txt @@ -19,13 +19,13 @@ _____________________________ The mapping to CG requires the correct protonation state of each residue at a given pH. We recommend using the `CHARMM-GUI server `_ with the **Glycan Reader & Modeler** to prepare your system, choosing the output naming scheme of AMBER for best compatibility. An account is required to access any of the CHARMM-GUI Input Generator modules, and it can take up to 24 hours to obtain one. -This example use the structure of glycoprotein `1GYA `_, using CHARMM-GUI server are obtained the files parm7 and rst7, this files are converted to pdb format with naming scheme of AMBER/GLYCAM using AmberTool as follow: +This example use the structure of glycoprotein `1GYA `_, using CHARMM-GUI server are obtained the files parm7 and rst7, these files are converted to pdb format with the naming scheme of AMBER/GLYCAM using AmberTool as follow: .. code-block:: bash ambpdb -p ./sirah.amber/tutorial/8/step3_input.parm7 -c ./sirah.amber/tutorial/8/step3_input.rst7 > 1GYA_glycam.pdb -From the file 1GYA_glycam.pdb generated delete the solvent, rename to 1GYA_glycam_NoW.pdb and then map the protonated atomistic to its CG representation: +From the file 1GYA_glycam.pdb generated delete the solvent, rename to 1GYA_glycam_NoW.pdb and then map the protonated atomistic structure to its CG representation: .. code-block:: bash @@ -48,7 +48,7 @@ The input file ``-i`` 1GYA_glycam_NoW.pdb contains the atomistic representation .. important:: - By default charged termini are used, but it is possible to set them neutral by renaming the residues from **s**\[code\] to **a**\[code\] (Nt-acetylated) or **m**\[code\] (Ct-amidated) after mapping to CG, where \[code\] is the root residue name in SIRAH. For example, to set a neutral N-terminal Histidine protonated at epsilon nitrogen (:math:`N_{\epsilon}`) rename it from “sHe” to “aHe”. + By default, charged termini are used. However, it is possible to set them neutral by renaming the residues from **s**\[code\] to **a**\[code\] (Nt-acetylated) or **m**\[code\] (Ct-amidated) after mapping to CG, where \[code\] is the root residue name in SIRAH. For example, to set a neutral N-terminal Histidine protonated at epsilon nitrogen (:math:`N_{\epsilon}`) rename it from “sHe” to “aHe”. Please check both PDBs structures using VMD: @@ -159,7 +159,7 @@ Make a new folder for the run: mkdir -p run; cd run The folder ``sirah.amber/tutorial/8/`` contains typical input files for energy minimization -(``em1_WT4.in`` and ``em2_WT4.in``), equilibration (``eq1_WT4.in`` and ``eq2_WT4.in``) and production (``md_WT4.in``) runs. Please check carefully the +(``em1_WT4.in`` and ``em2_WT4.in``), relaxation (or equilibration) (``eq1_WT4.in`` and ``eq2_WT4.in``) and production (``md_WT4.in``) runs. Please check carefully the input flags therein, in particular the definition of flag *chngmask=0* at *&ewald* section is **mandatory**. .. tip:: @@ -195,7 +195,7 @@ input flags therein, in particular the definition of flag *chngmask=0* at *&ewal pmemd.cuda -O -i ../sirah.amber/tutorial/8/em2_WT4.in -p ../1GYA_cg.prmtop -c ../1GYA_cg_em1.ncrst -o 1GYA_cg_em2.out -r 1GYA_cg_em2.ncrst & -**Solvent Equilibration (NPT):** +**Solvent Relaxation (or equlibration) in NPT:** .. code-block:: bash @@ -205,7 +205,7 @@ input flags therein, in particular the definition of flag *chngmask=0* at *&ewal Option **restraintmask=:'1-114'** in input file ``eq1_WT4.in`` must be set specifically for each system to embrace all glycoprotein’s residues. -**Soft equilibration to improve side chain and glycan solvation (NPT):** +**Soft Relaxation to improve side chain and glycan solvation (NPT):** .. code-block:: bash diff --git a/searchindex.js b/searchindex.js index b5c5e18..e92cbff 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["AMBER/Appendix", "AMBER/Tutorial-1", "AMBER/Tutorial-2", "AMBER/Tutorial-3", "AMBER/Tutorial-4", "AMBER/Tutorial-5", "AMBER/Tutorial-6", "AMBER/Tutorial-7", "AMBER/Tutorial-8", "AMBER/installation", "About SIRAH", "Analysis/Tutorial-basic", "Citation", "Developers", "FAQ", "Further reading", "GROMACS/Tutorial-1", "GROMACS/Tutorial-2", "GROMACS/Tutorial-3", "GROMACS/Tutorial-4", "GROMACS/Tutorial-5", "GROMACS/Tutorial-6", "GROMACS/installation-G", "SIRAHTools/Tutorial-tcl", "Tutorials amber", "Tutorials analysis", "Tutorials gromacs", "Tutorials namd", "Tutorials sirahtools", "index"], "filenames": ["AMBER/Appendix.rst", "AMBER/Tutorial-1.rst", "AMBER/Tutorial-2.rst", "AMBER/Tutorial-3.rst", "AMBER/Tutorial-4.rst", "AMBER/Tutorial-5.rst", "AMBER/Tutorial-6.rst", "AMBER/Tutorial-7.rst", "AMBER/Tutorial-8.rst", "AMBER/installation.rst", "About SIRAH.rst", "Analysis/Tutorial-basic.rst", "Citation.rst", "Developers.rst", "FAQ.rst", "Further reading.rst", "GROMACS/Tutorial-1.rst", "GROMACS/Tutorial-2.rst", "GROMACS/Tutorial-3.rst", "GROMACS/Tutorial-4.rst", "GROMACS/Tutorial-5.rst", "GROMACS/Tutorial-6.rst", "GROMACS/installation-G.rst", "SIRAHTools/Tutorial-tcl.rst", "Tutorials amber.rst", "Tutorials analysis.rst", "Tutorials gromacs.rst", "Tutorials namd.rst", "Tutorials sirahtools.rst", "index.rst"], "titles": ["Calculating ionic concentrations", "1.1. 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[0, 5, 7, 8, 14, 18, 21, 24, 26], "nomenclatur": [0, 14, 24], "conflict": [0, 14, 24], "user": [0, 5, 6, 7, 8, 9, 11, 14, 18, 20, 21, 22, 23, 24, 25, 26, 28], "ar": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "advis": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "check": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "modifi": [0, 5, 10, 11, 14, 18, 19, 21, 23, 24, 25, 26, 28], "requir": [0, 5, 6, 7, 8, 10, 11, 14, 18, 20, 21, 23, 25, 28], "type": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "compat": [0, 5, 8, 10, 11, 14, 18, 21, 24, 25, 26], "sourc": [0, 1, 2, 3, 4, 5, 6, 7, 8, 11, 23, 24, 25, 28], "f": [0, 1, 2, 3, 4, 5, 6, 7, 8, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "lipid11": [0, 14, 24], "17": [0, 14, 15, 24], "htmd": [0, 24], "gaff_lipid": [0, 24], "r": [0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 15, 17, 18, 21, 23, 24, 26, 28], "gaff": [0, 14, 24], "lipidbook": [0, 14, 24], "charmm_lipid": [0, 24], "charmm": [0, 5, 7, 8, 14, 17, 18, 21, 24, 26], "27": [0, 14, 24], "36": [0, 14, 15, 23, 24, 28], "gui": [0, 5, 7, 8, 14, 18, 21, 24, 26], "gromac": [0, 10, 11, 22, 23, 24, 25, 28], "membuild": [0, 14, 24], "vmd": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 16, 17, 18, 19, 20, 21, 22, 24, 26], "slipid": [0, 14, 24], "stockholm": [0, 24], "oplsa": [0, 24], "aa_2014_lipid": [0, 24], "all": [0, 1, 2, 3, 4, 5, 6, 8, 10, 11, 14, 15, 16, 18, 19, 20, 23, 24, 25, 26, 28, 29], "atom": [0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28, 29], "opl": [0, 5, 8, 14, 17, 18, 24, 26], "maciejewski": [0, 24], "ua_lipid": [0, 24], "unit": [0, 5, 8, 14, 23, 24, 28], "gromos43a1_lipid": [0, 24], "gromo": [0, 5, 8, 14, 17, 18, 24, 26], "43a1": [0, 24], "ckp": [0, 24], "gromos43a1": [0, 24], "s3_lipid": [0, 24], "s3": [0, 14, 24], "gromos53a6_lipid": [0, 24], "53a6": [0, 24], "tieleman_lipid": [0, 6, 7, 20, 21, 24, 26], "berger": [0, 24], "implement": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 17, 24, 26], "tieleman": [0, 24], "et": [0, 1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "al": [0, 1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "topologi": [0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28, 29], "pleas": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "report": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "bug": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "error": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "enhanc": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "request": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "through": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "issu": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "tracker": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "you": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "have": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "question": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "about": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "open": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "new": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "discuss": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "thi": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29], "tutori": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "show": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "how": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "perform": [1, 2, 4, 5, 6, 7, 8, 9, 11, 14, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "coars": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28, 29], "grain": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28, 29], "doubl": [1, 2, 14, 16, 23, 24, 26, 28], "strand": [1, 2, 11, 16, 24, 25, 26], "dna": [1, 2, 3, 4, 10, 11, 12, 14, 15, 16, 17, 19, 22, 23, 25, 28, 29], "us": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "born": [1, 3, 4, 24], "implicit": [1, 4, 23, 28], "solvent": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 14, 15, 16, 17, 19, 20, 21, 23, 25, 28, 29], "gb": [1, 3, 4, 24], "The": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "main": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "refer": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "dan": [1, 2, 4, 12, 13, 14, 15, 16, 18, 19, 24, 26], "latest": [1, 2, 4, 16, 19, 24, 26], "paramet": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 21, 23, 24, 25, 26, 28, 29], "those": [1, 2, 4, 5, 7, 8, 14, 16, 19, 24, 26], "here": [1, 2, 4, 11, 16, 19, 23, 24, 25, 26, 28], "machado": [1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 15, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "pantano": [1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 15, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "we": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "strongli": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "read": [1, 2, 3, 4, 5, 6, 7, 8, 11, 12, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "articl": [1, 2, 3, 4, 5, 6, 7, 8, 11, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "befor": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "start": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "set": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 15, 16, 17, 18, 19, 20, 21, 23, 25, 28, 29], "up": [1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29], "section": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29], "download": [1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21], "detail": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26], "sinc": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "i": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29], "rememb": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "replac": [1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 24, 26], "x": [1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 28], "file": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 14, 16, 17, 18, 19, 20, 22, 23, 25, 28], "correspond": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26], "found": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 24, 26], "sirah_": [1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 24, 26], "version": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "If": [1, 2, 3, 6, 7, 9, 11, 12, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "familiar": [1, 6, 9, 11, 22, 24, 25, 26], "stuff": [1, 2, 3, 4, 5, 6, 7, 8, 16, 18, 19, 20, 21, 24, 26], "recommend": [1, 5, 6, 7, 8, 9, 11, 14, 18, 20, 21, 22, 23, 24, 25, 26, 28], "first": [1, 2, 6, 7, 11, 14, 21, 23, 24, 25, 26, 28], "map": [1, 2, 3, 4, 5, 6, 7, 8, 10, 12, 14, 16, 18, 19, 20, 21, 23, 26, 28], "20": [1, 2, 5, 8, 14, 16, 24, 26], "mer": [1, 2, 16, 24, 26], "its": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "pl": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "pdb": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 22, 23, 24, 25, 28], "dna_cg": [1, 2, 3, 16, 24, 26], "contain": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "heavi": [1, 2, 3, 4, 6, 16, 19, 20, 24, 26], "compos": [1, 2, 3, 4, 6, 16, 19, 20, 24, 26], "while": [1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 16, 17, 18, 19, 20, 21, 24, 26], "output": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "preserv": [1, 2, 4, 5, 6, 8, 14, 16, 18, 19, 20, 24, 26], "few": [1, 2, 4, 6, 7, 11, 14, 16, 19, 20, 23, 24, 25, 26, 28], "them": [1, 2, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "both": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 18, 19, 20, 23, 24, 25, 26, 28], "basic": [1, 2, 3, 4, 5, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 28], "usag": [1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 28], "script": [1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28, 29], "learn": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 24, 25, 26], "other": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 28], "capabl": [1, 2, 3, 4, 5, 6, 7, 8, 10, 15, 16, 17, 18, 19, 20, 21, 24, 26, 29], "help": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "now": [1, 2, 3, 4, 5, 6, 7, 8, 11, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "just": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 18, 19, 20, 21, 23, 24, 26, 28], "normal": [1, 2, 3, 4, 5, 6, 7, 8, 16, 18, 19, 20, 21, 24, 26], "editor": [1, 2, 3, 4, 5, 6, 7, 8, 24], "creat": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "gensystem": [1, 2, 3, 4, 5, 6, 7, 8, 24], "includ": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28, 29], "follow": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "line": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "load": [1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 28], "addpath": [1, 2, 3, 4, 5, 6, 7, 8, 24], "leaprc": [1, 2, 3, 4, 5, 6, 7, 8, 24], "loadpdb": [1, 2, 3, 4, 5, 6, 7, 8, 24], "save": [1, 2, 3, 4, 5, 6, 7, 8, 11, 21, 23, 24, 25, 26, 28], "parm": [1, 2, 3, 4, 5, 6, 7, 14, 24], "saveamberparmnetcdf": [1, 2, 3, 4, 5, 6, 7, 8, 24], "prmtop": [1, 2, 3, 4, 5, 6, 7, 8, 14, 24], "ncrst": [1, 2, 3, 4, 5, 6, 7, 8, 14, 24], "exit": [1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 28], "quit": [1, 2, 3, 4, 5, 6, 7, 8, 11, 23, 24, 25, 28], "applic": [1, 2, 3, 4, 5, 6, 7, 8, 11, 12, 23, 24, 25, 28], "molecular": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "initi": [1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 21, 23, 24, 26, 28], "coordin": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 21, 23, 24, 25, 26, 28], "tleap": [1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 28], "warn": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 18, 19, 20, 21, 23, 24, 25, 26, 28], "messag": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 18, 19, 20, 21, 23, 24, 26, 28], "long": [1, 2, 3, 4, 5, 6, 7, 8, 12, 14, 16, 18, 19, 20, 21, 24, 26], "triangular": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 18, 19, 20, 21, 24, 26], "squar": [1, 2, 3, 4, 5, 6, 7, 8, 11, 16, 18, 19, 20, 21, 24, 25, 26], "bond": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "log": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 24, 26], "fine": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 18, 19, 20, 21, 24, 26], "expect": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 18, 19, 20, 21, 24, 26], "should": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "look": [1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "like": [1, 2, 3, 4, 5, 8, 12, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "sirah_vmdtk": [1, 2, 3, 4, 5, 6, 7, 8, 11, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "tcl": [1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "assign": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "default": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "radiu": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 24, 26], "unknown": [1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 24, 26], "right": [1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "ones": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "accord": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "It": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28, 29], "also": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "provid": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28, 29], "kit": [1, 2, 3, 4, 5, 6, 7, 8, 11, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "select": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "macro": [1, 2, 3, 4, 5, 6, 7, 8, 11, 16, 17, 18, 19, 20, 21, 24, 25, 26], "color": [1, 2, 3, 4, 5, 6, 7, 8, 11, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "method": [1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "backmap": [1, 2, 3, 4, 5, 6, 7, 8, 10, 12, 16, 17, 18, 19, 20, 21, 24, 26], "util": [1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "command": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "sirah_help": [1, 2, 3, 4, 5, 6, 7, 8, 11, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "tk": [1, 2, 3, 4, 5, 6, 7, 8, 11, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "consol": [1, 2, 3, 4, 5, 6, 7, 8, 11, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "access": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 16, 17, 19, 20, 21, 23, 24, 25, 28, 29], "manual": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "page": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "To": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "go": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "make": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 28], "mkdir": [1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 26], "p": [1, 2, 3, 4, 5, 6, 7, 8, 12, 14, 15, 16, 17, 18, 19, 20, 21, 24, 26], "cd": [1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 26], "pmemd": [1, 2, 3, 4, 5, 6, 7, 8, 14, 23, 24, 28], "gpu": [1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 16, 17, 18, 19, 20, 21, 24, 26, 29], "typic": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 24, 26], "energi": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 24, 26], "minim": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "em_gb": [1, 24], "equilibr": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 24, 26], "eq_gb": [1, 2, 3, 24], "product": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 24, 26], "md_gb": [1, 2, 3, 24], "carefulli": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 24, 26], "flag": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "therein": [1, 2, 3, 4, 5, 8, 16, 17, 18, 19, 20, 21, 24, 26], "some": [1, 2, 3, 4, 5, 6, 7, 8, 12, 14, 16, 18, 19, 20, 21, 23, 24, 26, 28, 29], "commonli": [1, 2, 3, 4, 5, 6, 7, 8, 24], "c": [1, 2, 3, 4, 5, 6, 7, 8, 12, 15, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "restart": [1, 2, 3, 4, 5, 6, 7, 8, 14, 24], "trajectori": [1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "These": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 18, 23, 24, 25, 26, 28], "execut": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 15, 18, 23, 24, 25, 26, 28], "cuda": [1, 2, 3, 4, 5, 6, 7, 8, 14, 23, 24, 28], "avail": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 28], "modul": [1, 2, 3, 4, 5, 6, 7, 8, 18, 21, 23, 24, 26, 28], "sander": [1, 2, 3, 4, 5, 6, 7, 8, 14, 24], "which": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28, 29], "cpu": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "find": [1, 2, 3, 4, 6, 7, 11, 20, 21, 23, 24, 25, 26, 28], "exampl": [1, 2, 3, 4, 5, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "within": [1, 2, 3, 4, 7, 10, 11, 12, 14, 15, 17, 18, 20, 21, 23, 24, 25, 26, 28, 29], "dna_cg_em": [1, 2, 16, 24, 26], "out": [1, 2, 3, 4, 5, 6, 7, 8, 14, 23, 24, 28, 29], "In": [1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "cours": [1, 2, 3, 24], "md": [1, 2, 3, 9, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28, 29], "cap": [1, 2, 3, 16, 24, 26], "mai": [1, 2, 3, 5, 6, 7, 8, 10, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "eventu": [1, 2, 3, 7, 14, 16, 24, 26], "separ": [1, 2, 3, 9, 16, 23, 24, 26, 28], "effect": [1, 2, 3, 14, 16, 18, 24, 26], "call": [1, 2, 3, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 24, 26], "helix": [1, 2, 3, 14, 16, 23, 24, 26, 28], "frai": [1, 2, 3, 16, 24, 26], "avoid": [1, 2, 3, 6, 7, 14, 16, 20, 21, 23, 24, 26, 28], "behavior": [1, 2, 3, 14, 23, 24, 28], "necessari": [1, 2, 3, 7, 11, 24, 25], "watson": [1, 2, 3, 16, 24, 26], "crick": [1, 2, 3, 16, 24, 26], "restraint": [1, 2, 3, 14, 16, 18, 24], "pair": [1, 2, 3, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 24, 26], "end": [1, 2, 3, 4, 16, 19, 20, 24, 26], "rst": [1, 2, 3, 24], "must": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 18, 21, 23, 24, 25, 26, 28], "symbol": [1, 2, 3, 9, 18, 22, 24, 26], "link": [1, 2, 3, 9, 10, 17, 18, 22, 24, 26, 29], "definit": [1, 2, 3, 5, 8, 9, 14, 17, 22, 24, 26], "ln": [1, 2, 3, 9, 18, 22, 24, 26], "": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "onli": [1, 2, 3, 11, 14, 23, 24, 25, 28], "restrain": [1, 2, 3, 5, 7, 8, 14, 18, 21, 24, 26], "format": [1, 2, 3, 7, 8, 10, 14, 24], "dna_cg_eq": [1, 2, 16, 24, 26], "nc": [1, 2, 3, 4, 5, 6, 7, 8, 24], "100n": [1, 2, 4, 16, 17, 19, 20, 24, 26], "dna_cg_md": [1, 2, 16, 24, 26], "anal": [1, 3, 4, 23, 24, 28], "part": [1, 2, 3, 4, 5, 6, 7, 8, 11, 16, 17, 18, 19, 20, 21, 24, 25, 26], "properli": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "embed": [2, 7, 17, 21, 24, 26], "explicit": [2, 5, 6, 7, 8, 10, 12, 16, 18, 19, 20, 21], "watfour": [2, 5, 6, 7, 8, 16, 18, 19, 20, 21, 24, 26], "info": [2, 5, 11, 14, 23, 24, 25, 28], "system": [2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 24, 25, 29], "charg": [2, 5, 8, 14, 18, 21, 23, 24, 26, 28], "add": [2, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 24, 26], "counterion": [2, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 24, 26], "nacl": [2, 5, 6, 7, 8, 16, 18, 19, 20, 21, 24, 26], "tune": [2, 5, 6, 7, 8, 24], "solut": [2, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "close": [2, 4, 5, 6, 8, 11, 14, 17, 19, 23, 25, 28], "best": [2, 5, 6, 7, 8, 18, 21, 23, 24, 26, 28], "hydrat": [2, 5, 6, 7, 8, 14, 24], "solvateoct": [2, 5, 8, 24], "wt4box": [2, 5, 6, 7, 8, 24], "7": [2, 5, 6, 8, 11, 14, 16, 17, 18, 19, 20, 23, 25, 28], "addionsrand": [2, 5, 6, 7, 8, 24], "naw": [2, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "88": [2, 24], "clw": [2, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "50": [2, 14, 23, 24, 28], "electrolyt": [2, 5, 6, 7, 8, 12, 16, 17, 18, 19, 20, 21, 24, 26], "speci": [2, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 24, 26], "na": [2, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 24, 26], "k": [2, 5, 6, 7, 8, 11, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "kw": [2, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "cl": [2, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 24, 26], "repres": [2, 3, 4, 5, 6, 7, 8, 10, 14, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28, 29], "solvat": [2, 5, 6, 7, 8, 12, 14, 15, 23, 24, 28], "One": [2, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "each": [2, 3, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "result": [2, 3, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "salt": [2, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 24, 26], "concentr": [2, 5, 6, 7, 8, 11, 16, 17, 18, 19, 20, 21, 25, 26], "see": [2, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "appendix": [2, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 26], "were": [2, 5, 6, 7, 8, 11, 12, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "ad": [2, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "em_wt4": [2, 24], "eq_wt4": [2, 24], "md_wt4": [2, 5, 8, 24], "particular": [2, 5, 8, 11, 24, 25], "chngmask": [2, 5, 8, 14, 24], "ewald": [2, 5, 8, 14, 24], "mandatori": [2, 5, 8, 14, 24], "npt": [2, 5, 8, 14, 24], "ref": [2, 5, 6, 7, 8, 24], "That": [2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 24, 25, 26], "analyz": [2, 5, 6, 7, 8, 10, 11, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "process": [2, 5, 6, 7, 8, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "account": [2, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "period": [2, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "boundari": [2, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "condit": [2, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "pbc": [2, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "echo": [2, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 24, 26], "autoimag": [2, 5, 6, 7, 8, 24], "ngo": [2, 5, 6, 7, 8, 24], "nquit": [2, 5, 6, 7, 8, 24], "cpptraj": [2, 5, 8, 14], "y": [2, 5, 6, 7, 8, 20, 23, 24, 26, 28], "dna_cg_md_pbc": [2, 16, 24, 26], "interact": [2, 3, 5, 6, 7, 8, 10, 11, 14, 21, 23, 24, 25, 26, 28, 29], "Then": [2, 11, 14, 17, 23, 24, 25, 26, 28], "appli": [3, 6, 7, 8, 14, 16, 17, 20, 21, 23, 24, 26, 28], "multiscal": [3, 10, 12, 14, 15, 23, 28, 29], "studi": [3, 9, 10, 14, 15, 24, 29], "protein": [3, 5, 6, 8, 10, 11, 12, 14, 15, 18, 22, 23, 25, 28, 29], "approach": [3, 10, 12, 17, 24, 26, 29], "bind": [3, 14, 24], "region": [3, 7, 11, 24, 25], "treat": [3, 5, 8, 14, 18, 24, 26], "an": [3, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "contextu": [3, 24], "level": [3, 5, 8, 10, 11, 12, 14, 15, 18, 20, 21, 24, 25, 26, 29], "human": [3, 24], "tata": [3, 24], "tbp": [3, 24], "1c9b": [3, 24], "bound": [3, 24], "box": [3, 11, 14, 16, 17, 18, 19, 20, 21, 23, 25, 26, 28], "promot": [3, 24], "64": [3, 6, 20, 24, 26], "13": [3, 12, 15, 24], "immunodefici": [3, 24], "viru": [3, 12, 15, 24], "hiv": [3, 24], "genbank": [3, 24], "k03455": [3, 24], "figur": [3, 7, 11, 21, 23, 24, 25, 26, 28], "consid": [3, 6, 7, 14, 20, 24, 26], "implicitli": [3, 24], "highlight": [3, 24], "orang": [3, 7, 21, 24, 26], "7nm": [3, 24], "yellow": [3, 23, 24, 28], "nucleotid": [3, 14, 23, 24, 28], "outsid": [3, 14, 20, 23, 24, 26, 28], "tbphiv": [3, 24], "32": [3, 5, 12, 24], "45": [3, 24], "110": [3, 8, 21, 24, 26], "123": [3, 24], "154": [3, 24], "dna_hyb": [3, 24], "option": [3, 5, 7, 8, 11, 14, 18, 21, 23, 24, 25, 26, 28], "buffer": [3, 24], "two": [3, 6, 11, 14, 20, 23, 24, 25, 26, 28], "side": [3, 5, 6, 7, 8, 10, 11, 14, 18, 21, 24, 25, 26], "interfac": [3, 11, 12, 14, 23, 24, 25, 28], "alwai": [3, 5, 8, 14, 18, 23, 24, 26, 28], "step": [3, 6, 7, 11, 14, 16, 18, 19, 20, 21, 23, 24, 25, 26, 28], "b": [3, 4, 11, 15, 18, 19, 23, 24, 25, 26, 28], "form": [3, 5, 11, 14, 15, 18, 21, 24, 25, 26], "parm14sb": [3, 24], "parmbsc0": [3, 24], "oldff": [3, 24], "ff14sb": [3, 14, 23, 24, 28], "10": [3, 14, 15, 20, 23, 24, 26, 28], "12": [3, 7, 11, 21, 23, 24, 25, 26, 28], "14": [3, 11, 14, 23, 24, 25, 28], "parm99sb": [3, 24], "bsc0": [3, 24], "ff99bsc0": [3, 24], "ff10": [3, 24], "ff12sb": [3, 24], "respect": [3, 5, 8, 11, 14, 18, 21, 23, 24, 25, 26, 28], "newest": [3, 24], "bsc1": [3, 24], "work": [3, 5, 8, 9, 10, 11, 12, 14, 17, 22, 23, 24, 25, 26, 28], "equal": [3, 24], "well": [3, 14, 17, 24, 26], "em_hyb": [3, 24], "eq_hyb": [3, 24], "md_hyb": [3, 24], "howev": [3, 6, 7, 9, 10, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "time": [3, 6, 7, 10, 11, 14, 23, 24, 25, 28, 29], "consum": [3, 6, 7, 24], "ow": [3, 6, 7, 17, 24, 26], "size": [3, 6, 7, 11, 14, 20, 23, 24, 25, 26, 28], "parallel": [3, 6, 7, 23, 24, 28], "dna_hyb_em": [3, 24], "dna_hyb_eq": [3, 24], "10n": [3, 24], "dna_hyb_md": [3, 24], "circular": [4, 19], "ccdna": [4, 19, 24, 26], "sed": [4, 19, 24, 26], "dcx": [4, 19, 24, 26], "cw5": [4, 19, 24, 26], "dgx": [4, 24], "100": [4, 14, 18, 21, 23, 24, 26, 28], "gw3": [4, 24], "ccdna_cg": [4, 19, 24, 26], "renam": [4, 5, 8, 14, 17, 19, 24, 26], "aw5": [4, 19, 24, 26], "tw5": [4, 19, 24, 26], "gw5": [4, 19, 24, 26], "aw3": [4, 24], "tw3": [4, 24], "cw3": [4, 24], "adenin": [4, 19, 24, 26], "thymin": [4, 19, 24, 26], "guanin": [4, 19, 24, 26], "cytosin": [4, 19, 24, 26], "extrem": [4, 19, 23, 24, 26, 28], "coval": [4, 10, 24, 29], "px": [4, 23, 24, 28], "c1x": [4, 24], "101": [4, 24], "200": [4, 24], "em_gbsa": [4, 24], "eq_gbsa": [4, 24], "md_gbsa": [4, 24], "ccdna_cg_em": [4, 19, 24, 26], "ccdna_cg_eq": [4, 19, 24, 26], "ccdna_cg_md": [4, 19, 24, 26], "darr\u00e9": [5, 8, 12, 13, 15, 16, 17, 18, 24, 26], "correct": [5, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "proton": [5, 7, 8, 10, 14, 18, 21, 23, 24, 26, 28], "state": [5, 7, 8, 10, 11, 14, 18, 21, 23, 24, 25, 26, 28], "given": [5, 7, 8, 11, 14, 18, 21, 24, 25, 26], "ph": [5, 7, 8, 14, 18, 21, 24, 26], "server": [5, 7, 8, 18, 21, 24, 26], "reader": [5, 7, 8, 18, 21, 24, 26], "manipul": [5, 7, 18, 21, 24, 26], "your": [5, 6, 7, 8, 9, 10, 11, 12, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "ani": [5, 7, 8, 11, 14, 17, 18, 21, 23, 24, 25, 26, 28], "take": [5, 6, 7, 8, 11, 18, 20, 21, 23, 24, 25, 26, 28], "24": [5, 7, 8, 18, 21, 24, 26], "hour": [5, 7, 8, 18, 21, 24, 26], "obtain": [5, 7, 8, 9, 18, 21, 24, 26], "one": [5, 7, 8, 11, 12, 18, 21, 23, 24, 25, 26, 28], "pdb2pqr": [5, 18, 21, 24, 26], "choos": [5, 7, 8, 11, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "scheme": [5, 6, 7, 8, 14, 18, 20, 21, 24, 26], "wa": [5, 6, 10, 11, 12, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "pqr": [5, 7, 18, 21, 24, 26], "featur": [5, 10, 11, 14, 18, 21, 23, 24, 25, 26, 28, 29], "Be": [5, 14, 17, 18, 21, 23, 24, 26, 28], "awar": [5, 8, 14, 17, 18, 21, 23, 24, 26, 28], "lack": [5, 18, 21, 24, 26], "mse": [5, 18, 21, 24, 26], "seleno": [5, 18, 21, 24, 26], "met": [5, 18, 21, 24, 26], "tpo": [5, 18, 21, 24, 26], "phosphoryl": [5, 18, 21, 24, 26], "thy": [5, 18, 21, 24, 26], "sep": [5, 18, 21, 24, 26], "ser": [5, 18, 21, 24, 26], "delet": [5, 8, 14, 18], "case": [5, 7, 8, 9, 11, 14, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "mutat": [5, 15, 18, 21, 24, 26], "unmodifi": [5, 18, 21, 24, 26], "submit": [5, 18, 21, 24, 26], "1crn": [5, 18, 24, 26], "1crn_cg": [5, 18, 24, 26], "pai": [5, 8, 18, 24, 26], "attent": [5, 8, 18, 24, 26], "when": [5, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "experiment": [5, 8, 10, 14, 18, 24, 26], "although": [5, 8, 10, 11, 14, 18, 24, 25, 26], "gmx": [5, 8, 14, 16, 17, 18, 19, 20, 21, 24, 26], "might": [5, 8, 18, 24, 26], "ambigu": [5, 8, 14, 18, 24, 26], "special": [5, 8, 14, 18, 24, 26], "regard": [5, 8, 14, 18, 24, 26], "lead": [5, 7, 8, 14, 18, 24, 26], "wrong": [5, 8, 14, 18, 24, 26], "For": [5, 6, 7, 8, 9, 11, 14, 17, 18, 21, 22, 23, 24, 25, 26, 28], "hi": [5, 8, 14, 18, 24, 26], "histidin": [5, 8, 14, 18, 24, 26], "epsilon": [5, 8, 14, 18, 24, 26], "nitrogen": [5, 8, 18, 24, 26], "n_": [5, 8, 18, 24, 26], "regardless": [5, 8, 14, 18, 24, 26], "actual": [5, 8, 14, 18, 24, 26], "placement": [5, 8, 14, 18, 24, 26], "similarli": [5, 8, 11, 14, 18, 24, 25, 26], "glutam": [5, 8, 14, 18, 24, 26], "aspart": [5, 8, 14, 18, 24, 26], "acid": [5, 8, 10, 14, 18, 23, 24, 26, 28, 29], "glh": [5, 8, 14, 18, 24, 26], "ash": [5, 8, 14, 18, 24, 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23, 24, 25, 26, 28, 29], "through": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "issu": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "tracker": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "you": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "have": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "question": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "about": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "open": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "new": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "discuss": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "thi": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29], "tutori": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "show": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "how": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "perform": [1, 2, 4, 5, 6, 7, 8, 9, 11, 14, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "coars": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28, 29], "grain": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28, 29], "doubl": [1, 2, 14, 16, 23, 24, 26, 28], "strand": [1, 2, 11, 16, 24, 25, 26], "dna": [1, 2, 3, 4, 10, 11, 12, 14, 15, 16, 17, 19, 22, 23, 25, 28, 29], "us": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "born": [1, 3, 4, 24], "implicit": [1, 4, 23, 28], "solvent": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 14, 15, 16, 17, 19, 20, 21, 23, 25, 28, 29], "gb": [1, 3, 4, 24], "The": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "main": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "refer": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "dan": [1, 2, 4, 12, 13, 14, 15, 16, 18, 19, 24, 26], "latest": [1, 2, 4, 16, 19, 24, 26], "paramet": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 21, 23, 24, 25, 26, 28, 29], "those": [1, 2, 4, 5, 7, 8, 14, 16, 19, 24, 26], "here": [1, 2, 4, 11, 16, 19, 23, 24, 25, 26, 28], "machado": [1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 15, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "pantano": [1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 15, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "we": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "strongli": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "read": [1, 2, 3, 4, 5, 6, 7, 8, 11, 12, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "articl": [1, 2, 3, 4, 5, 6, 7, 8, 11, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "befor": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "start": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "set": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 15, 16, 17, 18, 19, 20, 21, 23, 25, 28, 29], "up": [1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29], "section": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29], "download": [1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21], "detail": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26], "sinc": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "i": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29], "rememb": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "replac": [1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 24, 26], "x": [1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 28], "file": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 14, 16, 17, 18, 19, 20, 22, 23, 25, 28], "correspond": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26], "found": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 24, 26], "sirah_": [1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 24, 26], "version": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "If": [1, 2, 3, 6, 7, 9, 11, 12, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "familiar": [1, 6, 9, 11, 22, 24, 25, 26], "stuff": [1, 2, 3, 4, 5, 6, 7, 8, 16, 18, 19, 20, 21, 24, 26], "recommend": [1, 5, 6, 7, 8, 9, 11, 14, 18, 20, 21, 22, 23, 24, 25, 26, 28], "first": [1, 2, 6, 7, 11, 14, 21, 23, 24, 25, 26, 28], "map": [1, 2, 3, 4, 5, 6, 7, 8, 10, 12, 14, 16, 18, 19, 20, 21, 23, 26, 28], "20": [1, 2, 5, 8, 14, 16, 24, 26], "mer": [1, 2, 16, 24, 26], "its": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "pl": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "pdb": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 22, 23, 24, 25, 28], "dna_cg": [1, 2, 3, 16, 24, 26], "contain": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "heavi": [1, 2, 3, 4, 6, 16, 19, 20, 24, 26], "compos": [1, 2, 3, 4, 6, 16, 19, 20, 24, 26], "while": [1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 16, 17, 18, 19, 20, 21, 24, 26], "output": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "preserv": [1, 2, 4, 5, 6, 8, 14, 16, 18, 19, 20, 24, 26], "few": [1, 2, 4, 6, 7, 11, 14, 16, 19, 20, 23, 24, 25, 26, 28], "them": [1, 2, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "both": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 18, 19, 20, 23, 24, 25, 26, 28], "basic": [1, 2, 3, 4, 5, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 28], "usag": [1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 28], "script": [1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28, 29], "learn": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 24, 25, 26], "other": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 28], "capabl": [1, 2, 3, 4, 5, 6, 7, 8, 10, 15, 16, 17, 18, 19, 20, 21, 24, 26, 29], "help": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "now": [1, 2, 3, 4, 5, 6, 7, 8, 11, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "just": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 18, 19, 20, 21, 23, 24, 26, 28], "normal": [1, 2, 3, 4, 5, 6, 7, 8, 16, 18, 19, 20, 21, 24, 26], "editor": [1, 2, 3, 4, 5, 6, 7, 8, 24], "creat": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "gensystem": [1, 2, 3, 4, 5, 6, 7, 8, 24], "includ": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28, 29], "follow": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "line": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "load": [1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 28], "addpath": [1, 2, 3, 4, 5, 6, 7, 8, 24], "leaprc": [1, 2, 3, 4, 5, 6, 7, 8, 24], "loadpdb": [1, 2, 3, 4, 5, 6, 7, 8, 24], "save": [1, 2, 3, 4, 5, 6, 7, 8, 11, 21, 23, 24, 25, 26, 28], "parm": [1, 2, 3, 4, 5, 6, 7, 14, 24], "saveamberparmnetcdf": [1, 2, 3, 4, 5, 6, 7, 8, 24], "prmtop": [1, 2, 3, 4, 5, 6, 7, 8, 14, 24], "ncrst": [1, 2, 3, 4, 5, 6, 7, 8, 14, 24], "exit": [1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 28], "quit": [1, 2, 3, 4, 5, 6, 7, 8, 11, 23, 24, 25, 28], "applic": [1, 2, 3, 4, 5, 6, 7, 8, 11, 12, 23, 24, 25, 28], "molecular": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29], "initi": [1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 21, 23, 24, 26, 28], "coordin": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 21, 23, 24, 25, 26, 28], "tleap": [1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 28], "warn": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 18, 19, 20, 21, 23, 24, 25, 26, 28], "messag": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 18, 19, 20, 21, 23, 24, 26, 28], "long": [1, 2, 3, 4, 5, 6, 7, 8, 12, 14, 16, 18, 19, 20, 21, 24, 26], "triangular": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 18, 19, 20, 21, 24, 26], "squar": [1, 2, 3, 4, 5, 6, 7, 8, 11, 16, 18, 19, 20, 21, 24, 25, 26], "bond": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "log": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 24, 26], "fine": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 18, 19, 20, 21, 24, 26], "expect": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 18, 19, 20, 21, 24, 26], "should": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "look": [1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "like": [1, 2, 3, 4, 5, 8, 12, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "sirah_vmdtk": [1, 2, 3, 4, 5, 6, 7, 8, 11, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "tcl": [1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "assign": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "default": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "radiu": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 24, 26], "unknown": [1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 24, 26], "right": [1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "ones": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "accord": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "It": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28, 29], "also": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "provid": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28, 29], "kit": [1, 2, 3, 4, 5, 6, 7, 8, 11, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "select": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "macro": [1, 2, 3, 4, 5, 6, 7, 8, 11, 16, 17, 18, 19, 20, 21, 24, 25, 26], "color": [1, 2, 3, 4, 5, 6, 7, 8, 11, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "method": [1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "backmap": [1, 2, 3, 4, 5, 6, 7, 8, 10, 12, 16, 17, 18, 19, 20, 21, 24, 26], "util": [1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "command": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "sirah_help": [1, 2, 3, 4, 5, 6, 7, 8, 11, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "tk": [1, 2, 3, 4, 5, 6, 7, 8, 11, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "consol": [1, 2, 3, 4, 5, 6, 7, 8, 11, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "access": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 16, 17, 19, 20, 21, 23, 24, 25, 28, 29], "manual": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "page": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "To": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "go": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "make": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 28], "mkdir": [1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 26], "p": [1, 2, 3, 4, 5, 6, 7, 8, 12, 14, 15, 16, 17, 18, 19, 20, 21, 24, 26], "cd": [1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 26], "pmemd": [1, 2, 3, 4, 5, 6, 7, 8, 14, 23, 24, 28], "gpu": [1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 16, 17, 18, 19, 20, 21, 24, 26, 29], "typic": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 24, 26], "energi": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 24, 26], "minim": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "em_gb": [1, 24], "equilibr": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 24, 26], "eq_gb": [1, 2, 3, 24], "product": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 24, 26], "md_gb": [1, 2, 3, 24], "carefulli": [1, 2, 3, 4, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 24, 26], "flag": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "therein": [1, 2, 3, 4, 5, 8, 16, 17, 18, 19, 20, 21, 24, 26], "some": [1, 2, 3, 4, 5, 6, 7, 8, 12, 14, 16, 18, 19, 20, 21, 23, 24, 26, 28, 29], "commonli": [1, 2, 3, 4, 5, 6, 7, 8, 24], "c": [1, 2, 3, 4, 5, 6, 7, 8, 12, 15, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "restart": [1, 2, 3, 4, 5, 6, 7, 8, 14, 24], "trajectori": [1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "These": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 18, 23, 24, 25, 26, 28], "execut": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 15, 18, 23, 24, 25, 26, 28], "cuda": [1, 2, 3, 4, 5, 6, 7, 8, 14, 23, 24, 28], "avail": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 28], "modul": [1, 2, 3, 4, 5, 6, 7, 8, 18, 21, 23, 24, 26, 28], "sander": [1, 2, 3, 4, 5, 6, 7, 8, 14, 24], "which": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28, 29], "cpu": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "find": [1, 2, 3, 4, 6, 7, 11, 20, 21, 23, 24, 25, 26, 28], "exampl": [1, 2, 3, 4, 5, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "within": [1, 2, 3, 4, 7, 10, 11, 12, 14, 15, 17, 18, 20, 21, 23, 24, 25, 26, 28, 29], "dna_cg_em": [1, 2, 16, 24, 26], "out": [1, 2, 3, 4, 5, 6, 7, 8, 14, 23, 24, 28, 29], "In": [1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "cours": [1, 2, 3, 24], "md": [1, 2, 3, 9, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28, 29], "cap": [1, 2, 3, 16, 24, 26], "mai": [1, 2, 3, 5, 6, 7, 8, 10, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "eventu": [1, 2, 3, 7, 14, 16, 24, 26], "separ": [1, 2, 3, 9, 16, 23, 24, 26, 28], "effect": [1, 2, 3, 14, 16, 18, 24, 26], "call": [1, 2, 3, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 24, 26], "helix": [1, 2, 3, 14, 16, 23, 24, 26, 28], "frai": [1, 2, 3, 16, 24, 26], "avoid": [1, 2, 3, 6, 7, 14, 16, 20, 21, 23, 24, 26, 28], "behavior": [1, 2, 3, 14, 23, 24, 28], "necessari": [1, 2, 3, 7, 11, 24, 25], "watson": [1, 2, 3, 16, 24, 26], "crick": [1, 2, 3, 16, 24, 26], "restraint": [1, 2, 3, 14, 16, 18, 24], "pair": [1, 2, 3, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 24, 26], "end": [1, 2, 3, 4, 16, 19, 20, 24, 26], "rst": [1, 2, 3, 24], "must": [1, 2, 3, 4, 5, 6, 7, 8, 11, 14, 18, 21, 23, 24, 25, 26, 28], "symbol": [1, 2, 3, 9, 18, 22, 24, 26], "link": [1, 2, 3, 9, 10, 17, 18, 22, 24, 26, 29], "definit": [1, 2, 3, 5, 8, 9, 14, 17, 22, 24, 26], "ln": [1, 2, 3, 9, 18, 22, 24, 26], "": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "onli": [1, 2, 3, 11, 14, 23, 24, 25, 28], "restrain": [1, 2, 3, 5, 7, 8, 14, 18, 21, 24, 26], "format": [1, 2, 3, 7, 8, 10, 14, 24], "dna_cg_eq": [1, 2, 16, 24, 26], "nc": [1, 2, 3, 4, 5, 6, 7, 8, 24], "100n": [1, 2, 4, 16, 17, 19, 20, 24, 26], "dna_cg_md": [1, 2, 16, 24, 26], "anal": [1, 3, 4, 23, 24, 28], "part": [1, 2, 3, 4, 5, 6, 7, 8, 11, 16, 17, 18, 19, 20, 21, 24, 25, 26], "properli": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "embed": [2, 7, 17, 21, 24, 26], "explicit": [2, 5, 6, 7, 8, 10, 12, 16, 18, 19, 20, 21], "watfour": [2, 5, 6, 7, 8, 16, 18, 19, 20, 21, 24, 26], "info": [2, 5, 11, 14, 23, 24, 25, 28], "system": [2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 24, 25, 29], "charg": [2, 5, 8, 14, 18, 21, 23, 24, 26, 28], "add": [2, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 24, 26], "counterion": [2, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 24, 26], "nacl": [2, 5, 6, 7, 8, 16, 18, 19, 20, 21, 24, 26], "tune": [2, 5, 6, 7, 8, 24], "solut": [2, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "close": [2, 4, 5, 6, 8, 11, 14, 17, 19, 23, 25, 28], "best": [2, 5, 6, 7, 8, 18, 21, 23, 24, 26, 28], "hydrat": [2, 5, 6, 7, 8, 14, 24], "solvateoct": [2, 5, 8, 24], "wt4box": [2, 5, 6, 7, 8, 24], "7": [2, 5, 6, 8, 11, 14, 16, 17, 18, 19, 20, 23, 25, 28], "addionsrand": [2, 5, 6, 7, 8, 24], "naw": [2, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "88": [2, 24], "clw": [2, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "50": [2, 14, 23, 24, 28], "electrolyt": [2, 5, 6, 7, 8, 12, 16, 17, 18, 19, 20, 21, 24, 26], "speci": [2, 5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 24, 26], "na": [2, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 24, 26], "k": [2, 5, 6, 7, 8, 11, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "kw": [2, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "cl": [2, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 24, 26], "repres": [2, 3, 4, 5, 6, 7, 8, 10, 14, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28, 29], "solvat": [2, 5, 6, 7, 8, 12, 14, 15, 23, 24, 28], "One": [2, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "each": [2, 3, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "result": [2, 3, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "salt": [2, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 24, 26], "concentr": [2, 5, 6, 7, 8, 11, 16, 17, 18, 19, 20, 21, 25, 26], "see": [2, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "appendix": [2, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 26], "were": [2, 5, 6, 7, 8, 11, 12, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "ad": [2, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "em_wt4": [2, 24], "eq_wt4": [2, 24], "md_wt4": [2, 5, 8, 24], "particular": [2, 5, 8, 11, 24, 25], "chngmask": [2, 5, 8, 14, 24], "ewald": [2, 5, 8, 14, 24], "mandatori": [2, 5, 8, 14, 24], "npt": [2, 5, 8, 14, 24], "ref": [2, 5, 6, 7, 8, 24], "That": [2, 3, 4, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 24, 25, 26], "analyz": [2, 5, 6, 7, 8, 10, 11, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "process": [2, 5, 6, 7, 8, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "account": [2, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "period": [2, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "boundari": [2, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "condit": [2, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "pbc": [2, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "echo": [2, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 24, 26], "autoimag": [2, 5, 6, 7, 8, 24], "ngo": [2, 5, 6, 7, 8, 24], "nquit": [2, 5, 6, 7, 8, 24], "cpptraj": [2, 5, 8, 14], "y": [2, 5, 6, 7, 8, 20, 23, 24, 26, 28], "dna_cg_md_pbc": [2, 16, 24, 26], "interact": [2, 3, 5, 6, 7, 8, 10, 11, 14, 21, 23, 24, 25, 26, 28, 29], "Then": [2, 11, 14, 17, 23, 24, 25, 26, 28], "appli": [3, 6, 7, 8, 14, 16, 17, 20, 21, 23, 24, 26, 28], "multiscal": [3, 10, 12, 14, 15, 23, 28, 29], "studi": [3, 9, 10, 14, 15, 24, 29], "protein": [3, 5, 6, 8, 10, 11, 12, 14, 15, 18, 22, 23, 25, 28, 29], "approach": [3, 10, 12, 17, 24, 26, 29], "bind": [3, 14, 24], "region": [3, 7, 11, 24, 25], "treat": [3, 5, 8, 14, 18, 24, 26], "an": [3, 5, 6, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "contextu": [3, 24], "level": [3, 5, 8, 10, 11, 12, 14, 15, 18, 20, 21, 24, 25, 26, 29], "human": [3, 24], "tata": [3, 24], "tbp": [3, 24], "1c9b": [3, 24], "bound": [3, 24], "box": [3, 11, 14, 16, 17, 18, 19, 20, 21, 23, 25, 26, 28], "promot": [3, 24], "64": [3, 6, 20, 24, 26], "13": [3, 12, 15, 24], "immunodefici": [3, 24], "viru": [3, 12, 15, 24], "hiv": [3, 24], "genbank": [3, 24], "k03455": [3, 24], "figur": [3, 7, 11, 21, 23, 24, 25, 26, 28], "consid": [3, 6, 7, 14, 20, 24, 26], "implicitli": [3, 24], "highlight": [3, 24], "orang": [3, 7, 21, 24, 26], "7nm": [3, 24], "yellow": [3, 23, 24, 28], "nucleotid": [3, 14, 23, 24, 28], "outsid": [3, 14, 20, 23, 24, 26, 28], "tbphiv": [3, 24], "32": [3, 5, 12, 24], "45": [3, 24], "110": [3, 8, 21, 24, 26], "123": [3, 24], "154": [3, 24], "dna_hyb": [3, 24], "option": [3, 5, 7, 8, 11, 14, 18, 21, 23, 24, 25, 26, 28], "buffer": [3, 24], "two": [3, 6, 11, 14, 20, 23, 24, 25, 26, 28], "side": [3, 5, 6, 7, 8, 10, 11, 14, 18, 21, 24, 25, 26], "interfac": [3, 11, 12, 14, 23, 24, 25, 28], "alwai": [3, 5, 8, 14, 18, 23, 24, 26, 28], "step": [3, 6, 7, 11, 14, 16, 18, 19, 20, 21, 23, 24, 25, 26, 28], "b": [3, 4, 11, 15, 18, 19, 23, 24, 25, 26, 28], "form": [3, 5, 11, 14, 15, 18, 21, 24, 25, 26], "parm14sb": [3, 24], "parmbsc0": [3, 24], "oldff": [3, 24], "ff14sb": [3, 14, 23, 24, 28], "10": [3, 14, 15, 20, 23, 24, 26, 28], "12": [3, 7, 11, 21, 23, 24, 25, 26, 28], "14": [3, 11, 14, 23, 24, 25, 28], "parm99sb": [3, 24], "bsc0": [3, 24], "ff99bsc0": [3, 24], "ff10": [3, 24], "ff12sb": [3, 24], "respect": [3, 5, 8, 11, 14, 18, 21, 23, 24, 25, 26, 28], "newest": [3, 24], "bsc1": [3, 24], "work": [3, 5, 8, 9, 10, 11, 12, 14, 17, 22, 23, 24, 25, 26, 28], "equal": [3, 24], "well": [3, 14, 17, 24, 26], "em_hyb": [3, 24], "eq_hyb": [3, 24], "md_hyb": [3, 24], "howev": [3, 6, 7, 8, 9, 10, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "time": [3, 6, 7, 10, 11, 14, 23, 24, 25, 28, 29], "consum": [3, 6, 7, 24], "ow": [3, 6, 7, 17, 24, 26], "size": [3, 6, 7, 11, 14, 20, 23, 24, 25, 26, 28], "parallel": [3, 6, 7, 23, 24, 28], "dna_hyb_em": [3, 24], "dna_hyb_eq": [3, 24], "10n": [3, 24], "dna_hyb_md": [3, 24], "circular": [4, 19], "ccdna": [4, 19, 24, 26], "sed": [4, 19, 24, 26], "dcx": [4, 19, 24, 26], "cw5": [4, 19, 24, 26], "dgx": [4, 24], "100": [4, 14, 18, 21, 23, 24, 26, 28], "gw3": [4, 24], "ccdna_cg": [4, 19, 24, 26], "renam": [4, 5, 8, 14, 17, 19, 24, 26], "aw5": [4, 19, 24, 26], "tw5": [4, 19, 24, 26], "gw5": [4, 19, 24, 26], "aw3": [4, 24], "tw3": [4, 24], "cw3": [4, 24], "adenin": [4, 19, 24, 26], "thymin": [4, 19, 24, 26], "guanin": [4, 19, 24, 26], "cytosin": [4, 19, 24, 26], "extrem": [4, 19, 23, 24, 26, 28], "coval": [4, 10, 24, 29], "px": [4, 23, 24, 28], "c1x": [4, 24], "101": [4, 24], "200": [4, 24], "em_gbsa": [4, 24], "eq_gbsa": [4, 24], "md_gbsa": [4, 24], "ccdna_cg_em": [4, 19, 24, 26], "ccdna_cg_eq": [4, 19, 24, 26], "ccdna_cg_md": [4, 19, 24, 26], "darr\u00e9": [5, 8, 12, 13, 15, 16, 17, 18, 24, 26], "correct": [5, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "proton": [5, 7, 8, 10, 14, 18, 21, 23, 24, 26, 28], "state": [5, 7, 8, 10, 11, 14, 18, 21, 23, 24, 25, 26, 28], "given": [5, 7, 8, 11, 14, 18, 21, 24, 25, 26], "ph": [5, 7, 8, 14, 18, 21, 24, 26], "server": [5, 7, 8, 18, 21, 24, 26], "reader": [5, 7, 8, 18, 21, 24, 26], "manipul": [5, 7, 18, 21, 24, 26], "your": [5, 6, 7, 8, 9, 10, 11, 12, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "ani": [5, 7, 8, 11, 14, 17, 18, 21, 23, 24, 25, 26, 28], "take": [5, 6, 7, 8, 11, 18, 20, 21, 23, 24, 25, 26, 28], "24": [5, 7, 8, 18, 21, 24, 26], "hour": [5, 7, 8, 18, 21, 24, 26], "obtain": [5, 7, 8, 9, 18, 21, 24, 26], "one": [5, 7, 8, 11, 12, 18, 21, 23, 24, 25, 26, 28], "pdb2pqr": [5, 18, 21, 24, 26], "choos": [5, 7, 8, 11, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "scheme": [5, 6, 7, 8, 14, 18, 20, 21, 24, 26], "wa": [5, 6, 10, 11, 12, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "pqr": [5, 7, 18, 21, 24, 26], "featur": [5, 10, 11, 14, 18, 21, 23, 24, 25, 26, 28, 29], "Be": [5, 14, 17, 18, 21, 23, 24, 26, 28], "awar": [5, 8, 14, 17, 18, 21, 23, 24, 26, 28], "lack": [5, 18, 21, 24, 26], "mse": [5, 18, 21, 24, 26], "seleno": [5, 18, 21, 24, 26], "met": [5, 18, 21, 24, 26], "tpo": [5, 18, 21, 24, 26], "phosphoryl": [5, 18, 21, 24, 26], "thy": [5, 18, 21, 24, 26], "sep": [5, 18, 21, 24, 26], "ser": [5, 18, 21, 24, 26], "delet": [5, 8, 14, 18], "case": [5, 7, 8, 9, 11, 14, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28], "mutat": [5, 15, 18, 21, 24, 26], "unmodifi": [5, 18, 21, 24, 26], "submit": [5, 18, 21, 24, 26], "1crn": [5, 18, 24, 26], "1crn_cg": [5, 18, 24, 26], "pai": [5, 8, 18, 24, 26], "attent": [5, 8, 18, 24, 26], "when": [5, 7, 8, 11, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28], "experiment": [5, 8, 10, 14, 18, 24, 26], "although": [5, 8, 10, 11, 14, 18, 24, 25, 26], "gmx": [5, 8, 14, 16, 17, 18, 19, 20, 21, 24, 26], "might": [5, 8, 18, 24, 26], "ambigu": [5, 8, 14, 18, 24, 26], "special": [5, 8, 14, 18, 24, 26], "regard": [5, 8, 14, 18, 24, 26], "lead": [5, 7, 8, 14, 18, 24, 26], "wrong": [5, 8, 14, 18, 24, 26], "For": [5, 6, 7, 8, 9, 11, 14, 17, 18, 21, 22, 23, 24, 25, 26, 28], "hi": [5, 8, 14, 18, 24, 26], "histidin": [5, 8, 14, 18, 24, 26], "epsilon": [5, 8, 14, 18, 24, 26], "nitrogen": [5, 8, 18, 24, 26], "n_": [5, 8, 18, 24, 26], "regardless": [5, 8, 14, 18, 24, 26], "actual": [5, 8, 14, 18, 24, 26], "placement": [5, 8, 14, 18, 24, 26], "similarli": [5, 8, 11, 14, 18, 24, 25, 26], "glutam": [5, 8, 14, 18, 24, 26], "aspart": [5, 8, 14, 18, 24, 26], "acid": [5, 8, 10, 14, 18, 23, 24, 26, 28, 29], "glh": [5, 8, 14, 18, 24, 26], "ash": [5, 8, 14, 18, 24, 26], "otherwis": [5, 8, 14, 18, 23, 24, 26, 28], "thei": [5, 8, 14, 17, 18, 23, 24, 26, 28], "neg": [5, 8, 14, 18, 24, 26], "addit": [5, 8, 9, 10, 11, 12, 14, 15, 18, 23, 24, 25, 26, 28], "disulfid": [5, 8, 14, 18, 22, 24, 26], "cystein": [5, 8, 14, 18, 24, 26], "cy": [5, 8, 14, 18, 24, 26], "cyx": [5, 8, 14, 18, 24, 26], "kind": [5, 8, 14, 18, 24, 26], "situat": [5, 8, 14, 18, 24, 26], "need": [5, 7, 8, 11, 14, 18, 19, 21, 23, 24, 25, 26, 28], "ident": [5, 8, 14, 18, 24, 26], "back": [5, 8, 14, 16, 18, 19, 20, 21, 24, 26], "henc": [5, 8, 14, 18, 24, 26], "total": [5, 8, 11, 14, 18, 23, 24, 25, 26, 28], "same": [5, 7, 8, 10, 11, 14, 18, 20, 21, 23, 24, 25, 26, 28, 29], "sure": [5, 8, 14, 18, 23, 24, 26, 28], "sirah_prot": [5, 8, 14, 18, 24, 26], "By": [5, 6, 7, 8, 14, 16, 17, 18, 19, 20, 21, 23, 24, 26, 28], "termini": [5, 8, 11, 14, 24, 25], "neutral": [5, 8, 14, 18, 21, 23, 24, 26, 28], "code": [5, 6, 7, 8, 10, 14, 21, 23, 24, 26, 28, 29], "nt": [5, 8, 14, 24], "acetyl": [5, 8, 14, 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Build CG representations": [[5, "build-cg-representations"], [20, "build-cg-representations"], [24, "id37"], [26, "id39"]], "5.2. Prepare LEaP input": [[5, "prepare-leap-input"], [24, "id39"]], "5.3. Run LEaP": [[5, "run-leap"], [24, "id40"]], "5.4. Run the simulation": [[5, "run-the-simulation"], [20, "run-the-simulation"], [24, "id41"], [26, "id43"]], "5.5. Visualizing the simulation": [[5, "visualizing-the-simulation"], [20, "visualizing-the-simulation"], [24, "id42"], [26, "id44"]], "6.1. Build CG representations": [[6, "build-cg-representations"], [21, "build-cg-representations"], [24, "id46"], [26, "id49"]], "6.2. Prepare LEaP input": [[6, "prepare-leap-input"], [24, "id47"]], "6.3. Run LEaP": [[6, "run-leap"], [24, "id49"]], "6.4. Resize the box with CPPTRAJ": [[6, "resize-the-box-with-cpptraj"], [24, "resize-the-box-with-cpptraj"]], "6.5. Run the simulation": [[6, "run-the-simulation"], [24, "id50"]], "6.6. Visualizing the simulation": [[6, "visualizing-the-simulation"], [24, "id51"]], "7.1. Build CG representations": [[7, "build-cg-representations"], [24, "id56"]], "7.1.1. Embed the protein in a lipid bilayer": [[7, "embed-the-protein-in-a-lipid-bilayer"], [24, "embed-the-protein-in-a-lipid-bilayer"]], "7.1.2. Delete close contact lipid molecules": [[7, "delete-close-contact-lipid-molecules"], [24, "delete-close-contact-lipid-molecules"]], "7.2. Prepare LEaP input": [[7, "prepare-leap-input"], [24, "id58"]], "7.3. Run LEaP": [[7, "run-leap"], [24, "id59"]], "7.4. Resize the box with CPPTRAJ": [[7, "resize-the-box-with-cpptraj"], [24, "id61"]], "7.5. Run the simulation": [[7, "run-the-simulation"], [24, "id62"]], "7.6. Visualizing the simulation": [[7, "visualizing-the-simulation"], [24, "id63"]], "8.1. Build CG representations": [[8, "build-cg-representations"], [24, "id68"]], "8.2. Prepare LEaP input": [[8, "prepare-leap-input"], [24, "id71"]], "8.3. Run LEaP": [[8, "run-leap"], [24, "id72"]], "8.4. Run the simulation": [[8, "run-the-simulation"], [24, "id73"]], "8.5. Visualizing the simulation": [[8, "visualizing-the-simulation"], [24, "id74"]], "Required Software": [[9, "required-software"], [22, "required-software"], [24, "required-software"], [26, "required-software"]], "Prior knowledge": [[9, "prior-knowledge"], [22, "prior-knowledge"], [24, "prior-knowledge"], [26, "prior-knowledge"]], "Download and Setting up SIRAH": [[9, "download-and-setting-up-sirah"], [24, "download-and-setting-up-sirah"]], "About SIRAH": [[10, "about-sirah"]], "Advantages": [[10, "advantages"]], "Limitations": [[10, "limitations"]], "License": [[10, "license"]], "Acknowledgments": [[10, "acknowledgments"]], "Follow us": [[10, "follow-us"]], "Loading the Trajectory": [[11, "loading-the-trajectory"], [25, "loading-the-trajectory"]], "RMSD": [[11, "rmsd"], [25, "rmsd"]], "1.1 RMSD Visualizer Tool": [[11, "rmsd-visualizer-tool"], [25, "rmsd-visualizer-tool"]], "1.2. Tcl script": [[11, "tcl-script"], [25, "tcl-script"]], "RMSF": [[11, "rmsf"], [25, "rmsf"]], "Radius of gyration": [[11, "radius-of-gyration"], [25, "radius-of-gyration"]], "SASA": [[11, "sasa"], [25, "sasa"]], "VMD in text mode": [[11, "vmd-in-text-mode"], [23, "vmd-in-text-mode"], [25, "vmd-in-text-mode"], [28, "vmd-in-text-mode"]], "Citations": [[12, "citations"]], "Developers": [[13, "developers"], [13, "id1"]], "Former contributors": [[13, "former-contributors"]], "FAQs": [[14, "faqs"]], "General questions": [[14, "general-questions"]], "AMBER questions": [[14, "amber-questions"]], "GROMACS questions": [[14, "gromacs-questions"]], "Further Reading": [[15, "further-reading"]], "SIRAH Applications": [[15, "sirah-applications"]], "1.2. PDB to GROMACS format": [[16, "pdb-to-gromacs-format"], [26, "pdb-to-gromacs-format"]], "1.3. Solvate the system": [[16, "solvate-the-system"], [26, "solvate-the-system"]], "2.1. PDB to GROMACS format": [[17, "pdb-to-gromacs-format"], [26, "id9"]], "2.2. Solvate the system": [[17, "solvate-the-system"], [26, "id10"]], "2.3. Run the simulation": [[17, "run-the-simulation"], [26, "id11"]], "2.4. Visualizing the simulation": [[17, "visualizing-the-simulation"], [26, "id12"]], "3.2. PDB to GROMACS format": [[18, "pdb-to-gromacs-format"], [26, "id19"]], "3.3. Solvate the system": [[18, "solvate-the-system"], [26, "id20"]], "3.6. Calculate the solvent accessible surface (SAS)": [[18, "calculate-the-solvent-accessible-surface-sas"], [26, "calculate-the-solvent-accessible-surface-sas"]], "4.2. PDB to GROMACS format": [[19, "pdb-to-gromacs-format"], [26, "id31"]], "4.3. Solvate the system": [[19, "solvate-the-system"], [26, "id32"]], "5.2. PDB to GROMACS format": [[20, "pdb-to-gromacs-format"], [26, "id40"]], "5.3. Solvate the system": [[20, "solvate-the-system"], [26, "id41"]], "6.2. Embed the protein in a lipid bilayer": [[21, "embed-the-protein-in-a-lipid-bilayer"], [26, "embed-the-protein-in-a-lipid-bilayer"]], "6.2.1. Delete close contact lipid molecules": [[21, "delete-close-contact-lipid-molecules"], [26, "delete-close-contact-lipid-molecules"]], "6.3. PDB to GROMACS format": [[21, "pdb-to-gromacs-format"], [26, "id52"]], "6.4. Solvate the system": [[21, "solvate-the-system"], [26, "id53"]], "6.5. Generate position restraint files": [[21, "generate-position-restraint-files"], [26, "generate-position-restraint-files"]], "6.6. Run the simulation": [[21, "run-the-simulation"], [26, "id55"]], "6.7. Visualizing the simulation": [[21, "visualizing-the-simulation"], [26, "id56"]], "Download and setting SIRAH": [[22, "download-and-setting-sirah"], [26, "download-and-setting-sirah"]], "Visualization of CG systems": [[23, "visualization-of-cg-systems"], [28, "visualization-of-cg-systems"]], "SIRAH macros": [[23, "sirah-macros"], [28, "sirah-macros"]], "Structural analysis of CG systems": [[23, "structural-analysis-of-cg-systems"], [28, "structural-analysis-of-cg-systems"]], "Secondary structure analysis": [[23, "secondary-structure-analysis"], [28, "secondary-structure-analysis"]], "Backmapping analysis": [[23, "backmapping-analysis"], [28, "backmapping-analysis"]], "AMBER": [[24, "amber"]], "Setting up SIRAH": [[24, "setting-up-sirah"], [26, "setting-up-sirah"]], "1. DNA molecule in implicit solvent": [[24, "dna-molecule-in-implicit-solvent"]], "2. DNA molecule in explicit solvent": [[24, "dna-molecule-in-explicit-solvent"]], "3. Multiscale simulation in implicit solvent": [[24, "multiscale-simulation-in-implicit-solvent"]], "4. Closed circular DNA in implicit solvent": [[24, "closed-circular-dna-in-implicit-solvent"]], "5. Proteins in explicit solvent": [[24, "proteins-in-explicit-solvent"]], "6. Lipid bilayers in explicit solvent": [[24, "lipid-bilayers-in-explicit-solvent"]], "7. Membrane proteins in explicit solvent": [[24, "membrane-proteins-in-explicit-solvent"]], "8. Glycoprotein in explicit solvent": [[24, "glycoprotein-in-explicit-solvent"]], "Appendix": [[24, "appendix"]], "Basic analyses VMD": [[25, "basic-analyses-vmd"]], "GROMACS": [[26, "gromacs"]], "1. DNA molecule in explicit solvent": [[26, "dna-molecule-in-explicit-solvent"]], "2. Hybrid solvation": [[26, "hybrid-solvation"]], "3. Proteins in explicit solvent": [[26, "proteins-in-explicit-solvent"]], "4. Closed circular DNA in explicit solvent": [[26, "closed-circular-dna-in-explicit-solvent"]], "5. Lipid bilayers in explicit solvent": [[26, "lipid-bilayers-in-explicit-solvent"]], "6. Membrane proteins in explicit solvent": [[26, "membrane-proteins-in-explicit-solvent"]], "NAMD": [[27, "namd"]], "SIRAH tools": [[28, "sirah-tools"]], "Welcome to SIRAH FF documentation": [[29, "welcome-to-sirah-ff-documentation"]]}, "indexentries": {}}) \ No newline at end of file