GROMACS version: 2021.4
GROMACS modification: No
Hi everyone,
I’m trying to run a constant surface tension simulation using the following commands, but when I checked my trajectory, I noticed that the periodic images seem to overlap, which doesn’t make sense. My system consists of a surface with a water box above it and some ions. Also I have restrained all the atoms in the surface. Could you please help me identify what is wrong with my code? I have attached a screenshot of the surface and its periodic images.
Thanks!
title = OPLS Lysozyme NPT equilibration
; Run parameters
define = -DPOSRES ; Prevent S and C6 from moving
refcoord_scaling = No ; fix restraint
integrator = md ; leap-frog integrator
nsteps = 4500000 ; 2 * 4500000 = 9000000 ps (9 ns)
dt = 0.002 ; 2 fs
; Output control
nstxout = 0 ; suppress bulky .trr file by specifying
nstvout = 0 ; 0 for output frequency of nstxout,
nstfout = 0 ; nstvout, and nstfout
nstenergy = 500 ; save energies every 1.0 ps
nstlog = 500 ; update log file every 1.0 ps
nstxout-compressed = 500 ; save compressed coordinates every 1.0 ps
compressed-x-grps = System ; save the whole system
; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = System ; two coupling groups - more accurate
tau_t = 1 ; time constant, in ps
ref_t = 300 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = Berendsen ; Pressure coupling on in NPT
pcoupltype = surface-tension
tau_p = 5 ; time constant, in ps
ref_p = 0.01 1.0 ; reference pressure, x-y, z (in bar)
compressibility = 4.5e-5 0 ; isothermal compressibility, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off
