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 = 100 ; 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 #
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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