[gmx-users] Water spreading on graphene!
David van der Spoel
spoel at xray.bmc.uu.se
Sun Apr 21 09:42:04 CEST 2013
On 2013-04-20 22:17, sarupria wrote:
> Dear all,
> I have a graphene like surface (carbons on a hexagonal lattice with zero
> partial charges and some LJ parameters) with a drop of water placed on it.
> In principle, this is a hydrophobic surface and the drop should remain a
> droplet on it. However, surprisingly I am seeing that the drop is spreading
> within a 1 ns of the simulation. In the past I have done some similar
> simulations (with a different structure but basically zero partial charge
> surface and LJ) on which the drop remains a drop.
> Does any body have any ideas of what I may be doing wrong? Pasted below is
> my mdp and top file. Briefly, I am doing NVT simulation, PME for
> electrostatics, TIP3P water model, the surface is frozen and intra-surface
> interactions are excluded, the cut-off distances are 1 nm, velocity rescale
> thermostat (I tried both with the entire system coupled to the same
> thermostat and with sheet and water being coupled to different thermostats).
> Any suggestions are welcome.
> My analysis suggests this comes from the long range electrostatics because
> we have tested the same thing in LAMMPS. When we turn off PPPM and use
> cut-off based Coulomb (~5 nm) in LAMMPS (yes now we have changed the
> software) we don't see the drop spreading.
> I have done so many simulations and to have this problem stumps me!! Thanks
> for being helpful always.
Interesting, have you tried the cut-off approach in gromacs? Which
version are you running by the way? But how can the graphene have
partial charge? Or is it terminated with H atoms? You probably should
turn off the dispersion correction since this is not a homogeneous
system, but that can hardly be the cause.
> #### MDP file Start ####
> dt = 0.002 ; time step
> nsteps = 1000000 ; number of steps
> nstcomm = 10 ; reset c.o.m. motion
> comm_mode = Linear
> nstxout = 2000 ; write coords
> nstvout = 2000 ; write velocities
> nstlog = 500 ; print to logfile
> nstenergy = 250 ; print energies
> xtc_grps = System ; group crds written in xtc
> nstxtcout = 250 ; freq write xtc files
> nstlist = 10 ; update pairlist
> ns_type = grid ; pairlist method
> coulombtype = PME ; algorithm for Coulomb
> rvdw = 1.00 ; cut-off for vdw
> rcoulomb = 1.00 ; cut-off for coulomb
> rlist = 1.00 ; cut-off for nearest
> Tcoupl = V-rescale ; temp coupling scheme
> ref_t = 300.0 ; temp of system
> tc-grps = System ; system to thermocouple
> tau_t = 0.5 ; strength of thermocoupling
> Pcoupl = No ; scheme for pressure
> Pcoupltype = isotropic ; pressure geometry
> tau_p = 0.5 ; p-coupoling time
> compressibility = 4.5e-5 ; compressibility
> ref_p = 1.0 ; ref pressure
> DispCorr = EnerPres ; long range correction
> gen_vel = yes ; generate init. vel
> gen_temp = 280 ; init. temp.
> gen_seed = 372340 ; random seed
> constraints = hbonds ; constraining bonds with H
> constraint_algorithm = shake
> freeze_grps = GRO
> freezedim = Y Y Y
> energygrps = GRO
> energygrp_excl = GRO GRO
> #### MDP File End #####
> View this message in context: http://gromacs.5086.x6.nabble.com/Water-spreading-on-graphene-tp5007497.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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