Dear all,
I am trying to equilibrate a MnO2 surface (not cluster periodic). After the NVT run, I see that the surface is deformed. I was wondering what else can I add in my nvt.mdp to not encounter this problem?
I have mainly followed the examples in the forum for graphene/CNT growth.
title = MnO2 in H2O NVT equilibration
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000 ; 2 * 500000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 50 ; save coordinates every 0.10 ps
nstvout = 50 ; save velocities every 0.10 ps
nstenergy = 50 ; save energies every 0.10 ps
nstlog = 50 ; update log file every 0.10 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = none ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet
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 = SOL MnO ; three coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; 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
periodic-molecules = yes
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = 188888 ; generate a random seed
As per your mdp file, gen_vel = yes, means, you have generaed velocities in grompp according to a Maxwell distribution at temperature gen-temp [K], with random seed gen-seed. But wherever values U have used for gen_seed is not worthwhile (a/c to me). Better to change this value to -1 and try to check ur results.
Regards
Nandan
Dear Nanda Kumar,
Thank you for your kind reply. I have done that as well. I still find that my MnO2 surface twists itself like a ribbon. I am not sure what the cause of it.
I am a DFT person.
G
can u insert here image file of energy minimized and NVT equilibrated MnO2 surface or structure.
Dear Gangotri Dey,
Would you consider using Berendsen thermostat for equilibrating the system? It is known that it should not be used for production, since it is not accurate, but it usually helps equilibrating the systems. I do not know if it might help...
Cheers,
Mario
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