GROMACS version: 2018.1

GROMACS modification: No

I’m trying to do some simulations of water with tip4p/2005 model. First I did and NPT on the system until the equilibrium and now I want to run a NVE

I would like to modify the script below to do an NVE simulations. The script is for NPT simulations using Pcoupl and Tcoupl. It’s very easy to switch to NVT with Tcoupl=no, but the problem that I want to change it to NVE. I though that I should use Tcoupl=no, Pcoupl=no and some other options that I found in the manual, and this will be enough, but it looks like is not cause the energy not remains constant… Someone knows how to change properly the code or can give me some hints?

Thank you

José

; RUN CONTROL PARAMETERS

integrator = md

; Start time and timestep in ps

tinit = 0

dt = 0.001

nsteps = 400000

; For exact run continuation or redoing part of a run

init_step = 0

; Part index is updated automatically on checkpointing (keeps files separate)

simulation-part = 1

; mode for center of mass motion removal

comm-mode = linear

; number of steps for center of mass motion removal

nstcomm = 5

; group(s) for center of mass motion removal

comm-grps =

;freezegrps =

;freezedim =

; LANGEVIN DYNAMICS OPTIONS

; Friction coefficient (amu/ps) and random seed

bd-fric = 0

ld_seed = 232354

; ENERGY MINIMIZATION OPTIONS

; Force tolerance and initial step-size

emtol = 10

emstep = 0.01

; Max number of iterations in relax-shells

niter = 20

; Step size (ps^2) for minimization of flexible constraints

fcstep = 0

; Frequency of steepest descents steps when doing CG

nstcgsteep = 1000

nbfgscorr = 10

; TEST PARTICLE INSERTION OPTIONS

rtpi = 0.05

; OUTPUT CONTROL OPTIONS

; Output frequency for coords (x), velocities (v) and forces (f)

nstxout = 0

nstvout = 0

nstfout = 0

; Output frequency for energies to log file and energy file

nstlog = 10000

nstcalcenergy = 10000

nstenergy = 2000

; Output frequency and precision for .xtc file

nstxout-compressed = 200000

compressed-x-precision = 1000

; 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 =

; Selection of energy groups

energygrps =

; NEIGHBORSEARCHING PARAMETERS

; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)

cutoff-scheme = Verlet

; nblist update frequency

nstlist = 1

; ns algorithm (simple or grid)

ns_type = grid

; Periodic boundary conditions: xyz, no, xy

pbc = xyz

periodic_molecules = yes

; 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 = 0.95

; long-range cut-off for switched potentials

; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics

coulombtype = pme

coulomb-modifier = Potential-shift-Verlet

rcoulomb-switch = 0

rcoulomb = 0.95

; Relative dielectric constant for the medium and the reaction field

epsilon-r = 1

epsilon-rf = 0

; Method for doing Van der Waals

vdw-type = cut-off

vdw-modifier = Potential-shift-Verlet

; cut-off lengths

rvdw-switch = 0.85

rvdw = 0.95

; Apply long range dispersion corrections for Energy and Pressure

DispCorr = EnerPres

; Extension of the potential lookup tables beyond the cut-off

table-extension = 1

; Separate tables between energy group pairs

energygrp-table =

; Spacing for the PME/PPPM FFT grid

fourierspacing = 0.1

; 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

ewald-rtol = 1e-05

ewald-rtol-lj = 0.001

lj-pme-comb-rule = Geometric

ewald-geometry = 3d

epsilon-surface = 0

; IMPLICIT SOLVENT ALGORITHM

implicit-solvent = No

; GENERALIZED BORN ELECTROSTATICS

; Algorithm for calculating Born radii

gb-algorithm = Still

; Frequency of calculating the Born radii inside rlist

nstgbradii = 1

; Cutoff for Born radii calculation; the contribution from atoms

; between rlist and rgbradii is updated every nstlist steps

rgbradii = 1

; Dielectric coefficient of the implicit solvent

gb-epsilon-solvent = 80

; Salt concentration in M for Generalized Born models

gb-saltconc = 0

; Scaling factors used in the OBC GB model. Default values are OBC(II)

gb-obc-alpha = 1

gb-obc-beta = 0.8

gb-obc-gamma = 4.85

gb-dielectric-offset = 0.009

sa-algorithm = Ace-approximation

; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA

; The value -1 will set default value for Still/HCT/OBC GB-models.

sa-surface-tension = -1

; OPTIONS FOR WEAK COUPLING ALGORITHMS

; Temperature coupling

Tcoupl = v-rescale

nsttcouple = 1

nh-chain-length = 10

print-nose-hoover-chain-variables = no

; Groups to couple separately

tc-grps = system

; Time constant (ps) and reference temperature (K)

tau_t = 0.3

ref_t = 300

; pressure coupling

;Pcoupl = no

Pcoupl = parrinello-rahman

pcoupltype = isotropic

nstpcouple = 1

; Time constant (ps), compressibility (1/bar) and reference P (bar)

tau_p = 0.3

compressibility = 4.5e-5

ref_p = 1

; Scaling of reference coordinates, No, All or COM

refcoord-scaling = com

; OPTIONS FOR QMMM calculations

; SIMULATED ANNEALING

; Type of annealing for each temperature group (no/single/periodic)

annealing = no

; Number of time points to use for specifying annealing in each group

annealing-npoints =

; List of times at the annealing points for each group

annealing-time =

; Temp. at each annealing point, for each group.

annealing-temp =

; GENERATE VELOCITIES FOR STARTUP RUN

gen_vel = yes

gen_temp = 300

gen_seed = -1

; OPTIONS FOR BONDS

constraints = none

; Type of constraint algorithm

constraint-algorithm = lincs

; Do not constrain the start configuration

continuation = no

; Use successive overrelaxation to reduce the number of shake iterations

Shake-SOR = no

; Relative tolerance of shake

shake-tol = 1e-6

; Highest order in the expansion of the constraint coupling matrix

lincs-order = 4

; 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 = 30