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tutorial / walkthrough of restrained ensemble workflow
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eirrgang committed Dec 14, 2018
1 parent 4a706b7 commit 8f47786
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1,051 changes: 1,051 additions & 0 deletions examples/alanine-dipeptide/equil0.gro
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1,051 changes: 1,051 additions & 0 deletions examples/alanine-dipeptide/equil1.gro
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1,051 changes: 1,051 additions & 0 deletions examples/alanine-dipeptide/equil2.gro
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1,051 changes: 1,051 additions & 0 deletions examples/alanine-dipeptide/equil3.gro
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84 changes: 84 additions & 0 deletions examples/alanine-dipeptide/grompp.mdp
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; 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
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; 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
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