Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Gmxapi 30: tutorial / walkthrough #19

Open
wants to merge 2 commits into
base: devel
Choose a base branch
from
Open

Gmxapi 30: tutorial / walkthrough #19

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
150914a
tutorial / walkthrough of restrained ensemble workflow
eirrgang Jun 20, 2018
8ba891a
work in progress
eirrgang Dec 14, 2018
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1,051 changes: 1,051 additions & 0 deletions examples/alanine-dipeptide/equil0.gro
View file
Open in desktop

Large diffs are not rendered by default.

1,051 changes: 1,051 additions & 0 deletions examples/alanine-dipeptide/equil1.gro
View file
Open in desktop

Large diffs are not rendered by default.

1,051 changes: 1,051 additions & 0 deletions examples/alanine-dipeptide/equil2.gro
View file
Open in desktop

Large diffs are not rendered by default.

1,051 changes: 1,051 additions & 0 deletions examples/alanine-dipeptide/equil3.gro
View file
Open in desktop

Large diffs are not rendered by default.

84 changes: 84 additions & 0 deletions examples/alanine-dipeptide/grompp.mdp
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,84 @@
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
dt = 0.002
nsteps = 50000

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 250
nstvout = 5000
nstfout = 0
; Output frequency for energies to log file and energy file
nstlog = 100
nstcalcenergy = 100
nstenergy = 100
; Output frequency and precision for .xtc file
nstxout-compressed = 250
compressed-x-precision = 500
; This selects the subset of atoms for the compressed
; trajectory file. You can select multiple groups. By
; default, all atoms will be written.
compressed-x-grps = Protein

; NEIGHBORSEARCHING PARAMETERS
; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)
cutoff-scheme = Verlet
; nblist update frequency
nstlist = 20
Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,
; a value of -1 means: use rlist
verlet-buffer-tolerance = 0.005
; nblist cut-off
rlist = 1.0
; long-range cut-off for switched potentials

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = pme
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = V-rescale
nsttcouple = -1
; Groups to couple separately
tc-grps = protein water
; Time constant (ps) and reference temperature (K)
tau_t = 3.0 3.0
ref_t = 298 298
; pressure coupling
Pcoupl = Berendsen
Pcoupltype = Isotropic
nstpcouple = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 10.0
compressibility = 1e-4
ref_p = 1.0
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = No

; OPTIONS FOR BONDS
constraints = all-bonds
; Type of constraint algorithm
constraint_algorithm = Lincs
; Do not constrain the start configuration
continuation = no
lincs_order = 6
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter = 1
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs_warnangle = 90
; Convert harmonic bonds to morse potentials
morse = no

219 changes: 219 additions & 0 deletions examples/alanine-dipeptide/topol.top
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,219 @@
; Include forcefield parameters
#include "amber99sb-ildn.ff/forcefield.itp"

[ moleculetype ]
; Name nrexcl
Protein 3

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 ACE rtp ACE q 0.0
1 HC 1 ACE HH31 1 0.1123 1.008 ; qtot 0.1123
2 CT 1 ACE CH3 2 -0.3662 12.01 ; qtot -0.2539
3 HC 1 ACE HH32 3 0.1123 1.008 ; qtot -0.1416
4 HC 1 ACE HH33 4 0.1123 1.008 ; qtot -0.0293
5 C 1 ACE C 5 0.5972 12.01 ; qtot 0.5679
6 O 1 ACE O 6 -0.5679 16 ; qtot 0
; residue 2 ALA rtp ALA q 0.0
7 N 2 ALA N 7 -0.4157 14.01 ; qtot -0.4157
8 H 2 ALA H 8 0.2719 1.008 ; qtot -0.1438
9 CT 2 ALA CA 9 0.0337 12.01 ; qtot -0.1101
10 H1 2 ALA HA 10 0.0823 1.008 ; qtot -0.0278
11 CT 2 ALA CB 11 -0.1825 12.01 ; qtot -0.2103
12 HC 2 ALA HB1 12 0.0603 1.008 ; qtot -0.15
13 HC 2 ALA HB2 13 0.0603 1.008 ; qtot -0.0897
14 HC 2 ALA HB3 14 0.0603 1.008 ; qtot -0.0294
15 C 2 ALA C 15 0.5973 12.01 ; qtot 0.5679
16 O 2 ALA O 16 -0.5679 16 ; qtot 0
; residue 3 NME rtp NME q 0.0
17 N 3 NME N 17 -0.4157 14.01 ; qtot -0.4157
18 H 3 NME H 18 0.2719 1.008 ; qtot -0.1438
19 CT 3 NME CH3 19 -0.149 12.01 ; qtot -0.2928
20 H1 3 NME HH31 20 0.0976 1.008 ; qtot -0.1952
21 H1 3 NME HH32 21 0.0976 1.008 ; qtot -0.0976
22 H1 3 NME HH33 22 0.0976 1.008 ; qtot 0

[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
2 3 1
2 4 1
2 5 1
5 6 1
5 7 1
7 8 1
7 9 1
9 10 1
9 11 1
9 15 1
11 12 1
11 13 1
11 14 1
15 16 1
15 17 1
17 18 1
17 19 1
19 20 1
19 21 1
19 22 1

[ pairs ]
; ai aj funct c0 c1 c2 c3
1 6 1
1 7 1
2 8 1
2 9 1
3 6 1
3 7 1
4 6 1
4 7 1
5 10 1
5 11 1
5 15 1
6 8 1
6 9 1
7 12 1
7 13 1
7 14 1
7 16 1
7 17 1
8 10 1
8 11 1
8 15 1
9 18 1
9 19 1
10 12 1
10 13 1
10 14 1
10 16 1
10 17 1
11 16 1
11 17 1
12 15 1
13 15 1
14 15 1
15 20 1
15 21 1
15 22 1
16 18 1
16 19 1
18 20 1
18 21 1
18 22 1

[ angles ]
; ai aj ak funct c0 c1 c2 c3
1 2 3 1
1 2 4 1
1 2 5 1
3 2 4 1
3 2 5 1
4 2 5 1
2 5 6 1
2 5 7 1
6 5 7 1
5 7 8 1
5 7 9 1
8 7 9 1
7 9 10 1
7 9 11 1
7 9 15 1
10 9 11 1
10 9 15 1
11 9 15 1
9 11 12 1
9 11 13 1
9 11 14 1
12 11 13 1
12 11 14 1
13 11 14 1
9 15 16 1
9 15 17 1
16 15 17 1
15 17 18 1
15 17 19 1
18 17 19 1
17 19 20 1
17 19 21 1
17 19 22 1
20 19 21 1
20 19 22 1
21 19 22 1

[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
1 2 5 6 9
1 2 5 7 9
3 2 5 6 9
3 2 5 7 9
4 2 5 6 9
4 2 5 7 9
2 5 7 8 9
2 5 7 9 9
6 5 7 8 9
6 5 7 9 9
5 7 9 10 9
5 7 9 11 9
5 7 9 15 9
8 7 9 10 9
8 7 9 11 9
8 7 9 15 9
7 9 11 12 9
7 9 11 13 9
7 9 11 14 9
10 9 11 12 9
10 9 11 13 9
10 9 11 14 9
15 9 11 12 9
15 9 11 13 9
15 9 11 14 9
7 9 15 16 9
7 9 15 17 9
10 9 15 16 9
10 9 15 17 9
11 9 15 16 9
11 9 15 17 9
9 15 17 18 9
9 15 17 19 9
16 15 17 18 9
16 15 17 19 9
15 17 19 20 9
15 17 19 21 9
15 17 19 22 9
18 17 19 20 9
18 17 19 21 9
18 17 19 22 9

[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3
2 7 5 6 4
5 9 7 8 4
9 17 15 16 4
15 19 17 18 4

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "amber99sb-ildn.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif

; Include topology for ions
#include "amber99sb-ildn.ff/ions.itp"

[ system ]
; Name
Protein

[ molecules ]
; Compound #mols
Protein 1
SOL 342
Loading