GROMACS version: 2021.3-MODIFIED
GROMACS modification: Yes
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Hello,
I am currently trying to simulate water at a metal interface and to do this, I have considered using freeze groups, but opted out of it due to concerns over energy exclusions so I settled on using strong positional restraints on the metal atoms. The problem is that during the NPT equilibration, with pbc, a vacuum is made and there is a large volume both above and below the solvent. I have been trying ways to fix it, but nothing seems to work? Are there any suggestions? Attached below is the mdp file:
;PREPROCESSING
define = -DPOSRES
;
;RUN CONTROLS
integrator = md ; USE MD
dt = 0.001 ; TIME STEP = 0.002 ps , 2 fs
nsteps = 4000000 ; TIME = dt * nsteps =
;
;OUTPUT CONTROLS
nstlog = 1000
nstxout = 100000
nstvout = 100000
nstfout = 1000
nstcalcenergy = 1000
nstenergy = 1000
;
; NEIGHBOR SEARCHING
cutoff-scheme = Verlet ; NEIGHBOR SEARCHING TYPE
nstlist = 20
rlist = 1.2
;
; COUMLOMBIC ELECTROSTATICS
coulombtype = pme ; COULOMB TYPE
rcoulomb = 1.2
;
; VAN DER WAALS FORCES
vdwtype = Cut-off ; VDW TYPE
vdw-modifier = Force-switch
rvdw_switch = 1.0
rvdw = 1.2
;
; TEMPERATURE COUPLING
tcoupl = V-rescale ; TEMP TYPE
tc_grps = system
tau_t = 1.0 ; TEMP TIME CONSTANT
ref_t = 300 ; TEMP REFERENCE
;
; PRESSURE COUPLING
pcoupl = C-rescale ; P-SCHEME (BREN) = LESS ACC, FAST (Par-Nell) = MORE ACC, SLOW
pcoupltype = isotropic ; P-TYPE
tau_p = 5.0 ; P-TIME CONSTANT
compressibility = 4.5e-5 ; ONLY ALLOWED TO FLUCTUATE IN THE Z DIRECTION
ref_p = 1.0
;
nstcomm = 100
comm_mode = linear
;comm-grps = SOL IPT
; VELOCITY GENERATION
gen-vel = yes
gen-temp = 300 ; 200K T then work up to 300K
gen-seed = -1 ; RANDOM SEED FOR GENERATOR
;
refcoord-scaling = all
; PERIODIC BOUNDARY CONDITIONS
pbc = xyz ; PRETTY MUCH ALWAYS USE PBC