[gmx-users] peculiar water behavior

[Chetan Mahajan]

One more important observation that I forgot to share:

With water moving from one side of the crystal slab to other side (through
periodic boundaries), crystal slab moves in the same direction (after
water) to fill the void in the box. I am using "com" refcoord-scaling.

Thanks
Chetan


On Thu, Jun 12, 2014 at 10:15 PM, Chetan Mahajan <chetanvm10 at gmail.com>
wrote:

> 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.
>
> Thanks
> Chetan
>
> 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
>
>