From 2b3f17fa0c03cac15e407c3386169be903f402c8 Mon Sep 17 00:00:00 2001 From: luciannahss Date: Fri, 13 Dec 2024 15:55:18 -0300 Subject: [PATCH] NAMD_correction --- docs/source/NAMD/Tutorial-1.rst | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/docs/source/NAMD/Tutorial-1.rst b/docs/source/NAMD/Tutorial-1.rst index 7182b3f..6581419 100644 --- a/docs/source/NAMD/Tutorial-1.rst +++ b/docs/source/NAMD/Tutorial-1.rst @@ -199,7 +199,7 @@ Run the VMD script to generate the pdb restriction file: .. code-block:: bash - vmd -dispdev text –e restraints.tcl + vmd -dispdev text -e restraints.tcl 1.5. Run the simulation @@ -218,7 +218,7 @@ Copy the input files to the folder: .. code-block:: bash - cp sirah.amber/tutorial/NAMD/1/NAMD2/*.conf . + cp ../sirah.amber/tutorial/NAMD/1/NAMD2/*.conf . The folder ``sirah.amber/tutorial/NAMD/1/NAMD2`` contains typical input files for energy minimization (``em1.conf`` and ``em2.conf``), heating (``heat.conf``), equilibration (``eq1.conf`` and ``eq2.conf``) and production (``md.conf``) runs. Please carefully review the input files, paying especially attention to the cell dimension values, names, and restrictions. @@ -300,6 +300,10 @@ The folder ``sirah.amber/tutorial/NAMD/1/NAMD2`` contains typical input files fo 1.5.2 NAMD3 ~~~~~~~~~~~~~ +.. warning:: + + Point release 3.0.1 fixes potentially impactful bugs in 3.0. All users are strongly encouraged to upgrade to this version. + Make a new folder for the run: .. code-block:: bash @@ -310,7 +314,7 @@ Copy the input files to the folder: .. code-block:: bash - cp sirah.amber/tutorial/NAMD/1/NAMD3/*.conf . + cp ../sirah.amber/tutorial/NAMD/1/NAMD3/*.conf . The folder ``sirah.amber/tutorial/NAMD/1/NAMD3`` contains typical input files for energy minimization (``em1.conf`` and ``em2.conf``), heating (``heat.conf``), equilibration (``eq1.conf`` and ``eq2.conf``) and production (``md.conf``) runs. Please carefully review the input files, paying especially attention to the cell dimension values, names, and restrictions. @@ -559,7 +563,7 @@ For ``eq1.conf``: # Constraints of protein if {1} { ;# If 1 read the block constraints on ;# Turns on constraints - consref your_restraints.pdb ;# Reference PDB file for constraint positions + consref your_restraints.coor ;# Reference PDB file for the last position (last_step.coor) conskfile your_restraints.pdb ;# File containing constraint force constants constraintScaling 1 ;# Scaling factor for constraint forces consexp 2 ;# Exponent for constraint potential @@ -577,7 +581,7 @@ For ``eq2.conf``: # Constraints of protein if {1} { ;# If 1 read the block constraints on ;# Turns on constraints - consref your_restraints.pdb ;# Reference PDB file for constraint positions + consref your_restraints.coor ;# Reference PDB file for the last position (last_step.coor) conskfile your_restraints.pdb ;# File containing constraint force constants constraintScaling 0.1 ;# Scaling factor for constraint forces consexp 2 ;# Exponent for constraint potential