GROMACS version: 2023
GROMACS modification: No
I’m trying to simulate the diffusion of methanol in the MOF ZIF-8. For this, I am using the Amber GAFF2 force field, since later I will need to introduce paracetamol molecules inside the MOF. I found the Amber parameters for methanol and tried to simulate a box containing only methanol thus performing energy minimization, NVT, and NPT and in the end, using:
gmx energy -f npt.edr -o density.xvg
What I obtain is a density lower than the experimental one (740 Kg/m³ vs. 786 Kg/m³; the experimental density reference is lower because I am simulating at 300K).
How can I resolve this issue? I would like the methanol to be as close as possible to the experimental data. Please let me know, thanks.
This is the .mdp file for NPT:
; VARIOUS PREPROCESSING OPTIONS
include = -I…/top
define =
; RUN CONTROL PARAMETERS
integrator = md
dt = 0.002
nsteps = 100000000 ; 200 ns
comm-mode = Linear
nstcomm = 20
comm-grps = MOL
; OUTPUT CONTROL OPTIONS
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 10000 ; 10 ps
nstcalcenergy = 20
nstenergy = 10000 ; 10 ps
nstxout-compressed = 10000 ; 10 ps
; NEIGHBORSEARCHING PARAMETERS
cutoff-scheme = Verlet
nstlist = 10
ns_type = grid
pbc = xyz
periodic-molecules = yes
rlist = 1.0
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = PME
rcoulomb = 1.0
vdwtype = Cut-off
rvdw = 1.0
DispCorr = EnerPres
; EWALD/PME/PPPM parameters
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-05
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = v-rescale
tc-grps = MOL
tau_t = 1.0
ref_t = 300
; pressure coupling
pcoupl = Berendsen
pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
refcoord-scaling = No
; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel = no
gen-temp = 300
gen-seed = 3532
; OPTIONS FOR BONDS
constraints = h-bonds
constraint_algorithm = lincs
continuation = yes
; ENERGY GROUP EXCLUSIONS
energygrp-excl =
; COM PULLING
pull = no
; Free energy variables
free-energy = no
; Non-equilibrium MD stuff
acc-grps =
accelerate =
freezegrps =
freezedim =