GROMACS version:
GROMACS modification: Yes/No
Here post your question
I am doing a simulation with a Graphene sheet with solvent. I want to make the graphene freeze in its initial position but after heating it is moving up. Below I have attached the mdp file and initial and after-heating snap. Can anyone please suggest what I need to impose to make the graphene sheet frozen in its position?
mdp file,
title = Graphene-LiPF6-EC Heating
;define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; Stochastic or velocity Langevin dynamics
nsteps = 1000000 ; 1 * 1000000 = 1000 ps
dt = 0.001 ; 1 fs
; Output control
nstxout = 500 ; save coordinates every 1.0 ps
nstvout = 500 ; save velocities every 1.0 ps
nstenergy = 500 ; save energies every 1.0 ps
nstlog = 500 ; update log file every 1.0 ps
; Bond parameters
continuation = no ; first dynamics run
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
; Nonbonded settings
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 10 fs, largely irrelevant with Verlet
rlist = 0.6
vdwtype = cutoff
vdw-modifier = Potential-switch
rvdw-switch = 0.4
rvdw = 0.6
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
rcoulomb = 0.6 ; short-range electrostatic cutoff (in nm)
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
DispCorr = EnerPres ; account for cut-off vdW scheme
; Temperature coupling is on
tcoupl = Nose-Hoover ; More accurate thermostat
tc-grps = GRA RES2 RES3 RES4 ; two coupling groups - more accurate
tau_t = 0.2 0.2 0.2 0.2 ; time constant, in ps
ref_t = 298 298 298 298 ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 298 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
;nstcomm = 100
;comm_mode = linear
;comm_grps = SYSTEM
; To freeze molecule
freezegrps = GRA
freezedim = Y Y Y
Thanks in Advance.