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 *Thank you* *Gangotri Dey* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.