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Dear Gromacs Users,
I am doing the multi-layer graphene sheet simulation but after the minimization, on heating, the graphene sheet layers are not maintaining the aligned conformation. So what I need to do or impose to maintain the alignment, please advise me.
Heating mdp file;
title = Heating
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; Stochastic or velocity Langevin dynamics
nsteps = 2000000 ; 1 * 2000000 = 2000 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 = 1.2
vdwtype = cutoff
vdw-modifier = Potential-switch
rvdw-switch = 1.0
rvdw = 1.2
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
rcoulomb = 1.2 ; 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 = system ; two coupling groups - more accurate
tau_t = 0.2 ; time constant, in ps
ref_t = 300 ; 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 = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
Thanks in advance