[gmx-users] peculiar water behavior

Chetan Mahajan chetanvm10 at gmail.com
Fri Jun 13 05:15:21 CEST 2014

Dear All,

I am simulating TiO2 crystal solvated by water  and ions like sodium and
formate. I am observing one peculiar thing, and I would like to rectify
that. I have initial structure of crystal slab at the center of the box
elongated in z-direction and almost equal boxlength on both the sides, with
a gap of 1 nm between slab surface and first layer of water close to slab.
 This space is kept to avoid water going on the sides of the crystal during
equilibration. This was a minor information. Now, the main observation is
that during NPT equilibration, water from one side of the slab enters the
other opposite side of the slab (using periodic conditions) so that
boxlengths on both sides of the slab are very different at the end of
equilibration. Is this an artifact of pressure coupling? Following is my
equilibration .mdp file. I have tried varying the compressibility and tau-p
parameters in the following file. e.g. zero compressibility in x/y
direction or tau-p reduced to 3.
No success.

I look forward to hearing from you. I would ideally want water to not leave
the box.


title                    = NPTequilibration of  ligand_nanop-anatase-tio2
integrator               = md-vv
dt                       = 0.001
nsteps                   = 1000000
nstxout                  = 1000
nstvout                  = 1000
nstlog                   = 1000
nstenergy                = 1000
nstxtcout                = 1000
nstlist                  = 1
ns-type                  = grid
rlist                    = 1.0
vdwtype                  = user
coulombtype              = pme
rcoulomb                 = 1.0
rvdw                     = 1.0
energygrps               = Ti OT OW c h5 o HW Na
energygrp-table          = Ti Ti OT OT Ti OT Ti OW OT c OT h5 OT o
tcoupl                   = Berendsen
tc-grps                  = System
tau-t                    = 0.1
ref-t                    = 300
Pcoupl                   = Berendsen
pcoupltype               = semiisotropic
tau-p                    = 5.0 5.0
compressibility          = 4.5e-5 4.5e-5
ref-p                    = 1.0 1.0
refcoord-scaling         = com
gen-vel                  = yes
gen-temp                 = 300
gen-seed                 = 173529

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