[gmx-users] Water spreading on graphene!

sarupria sapna.sarupria at gmail.com
Sat Apr 20 22:17:32 CEST 2013

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. 


#### 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 ##### 

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