[gmx-users] Water spreading on graphene!

[David van der Spoel]

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.

>
> Sapna
>
> #### 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
> neighbor
> 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
> coupling
> 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