I did not quite understand your comment. However, I am trying my best to answer it. I have a surface MnO2 model. I have solvated the structure in all 3 directions. After that, I minimize it and run NVT simulation with the parameters as mentioned. However, I see that there is a deformation of the surface and it does not remain a flat surface. Instead, it curls like a ribbon. This should not be the case. Hence, I am wondering what are the factors that can lead to this deformation? Are the parameters in the NVT simulation good enough or else there is a problem that I cannot see.
G *Thank you* *Gangotri Dey* Postdoctoral Associate Rutgers University New Brunswick Chemistry and Chemical Biology 174 Frelinghuysen Road, Piscataway, NJ 08854 Phone: +16092162254 On Mon, Aug 7, 2017 at 5:04 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > 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 <holyriv...@gmail.com> 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 gmx-users-requ...@gromacs.org. > > > -- > 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. > -- 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.