Hi, Are you trying to implement a model that you know is capable of produce a surface that does not deform in unexpected ways?
Mark On Mon, 7 Aug 2017 16:35 gangotri dey <[email protected]> wrote: > Dear all, > > I am trying to equilibrate a MnO2 surface (not cluster but periodic). I > have solvated the surface with water in all 3 directions. 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* > Postdoctoral Associate > Rutgers University New Brunswick > Chemistry and Chemical Biology > 174 Frelinghuysen Road, Piscataway, NJ 08854 > Phone: +16092162254 > -- > 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 [email protected]. > -- 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 [email protected].
