[gmx-users] analyze diffusion of water in first hydration shell

[Tsjerk Wassenaar]

Hi Pratibha,

I can't think of a simple solution using Gromacs' tools. Sorry.

Cheers,

Tsjerk



On Mon, Aug 18, 2014 at 11:31 AM, pratibha kapoor <kapoorpratibha7 at gmail.com
> wrote:

> Thanks Tsjerk for clearing my doubt.
> Is there any other inbuild function which can serve my purpose?
>
> Thanks
> Pratibha
>
>
> > Hi Pratibha,
> >
> > Unfortunately, that is not going to work. trjorder puts the closest water
> > molecule first in the output trajectory. But the closest one at time t
> need
> > not be the same as the closest one at time t+dt. So the MSD will be
> > meaningless.
> >
> > Cheers,
> >
> > Tsjerk
> >
> >
> > On Sun, Aug 17, 2014 at 11:20 AM, pratibha kapoor <
> > kapoorpratibha7 at gmail.com
> > > wrote:
> >
> > > Hi users,
> > >
> > > I would like to calculate diffusion of water molecules in the first
> > > hydration shell (say 0.4nm around protein). I have used trjorder
> command
> > > as:
> > > trjorder -f *.xtc -s *.tpr -o ordered.xtc -r 0.4
> > > Can I directly use
> > > g_msd -f ordered.xtc -s *.tpr
> > > after that to calculate diffusion of water molecules closest to
> protein?
> > I
> > > guess this would serve the purpose and there is no need to specifically
> > add
> > > n closest water in index group (Please correct me if I am wrong). But
> > then
> > > what does following line mean (line copied from trjorder -h):
> > >
> > >  "When an index group of the first n waters is made, the ordered
> > trajectory
> > > can be used with any Gromacs program to analyze the n closest waters."
> > >
> > > Based on reading previous posts on the mailing list, I realise that for
> > msd
> > > calculation we have to use *.xtc with no pbc applied. In above case
> won't
> > > trjorder automatically uses pbc yes condition. In this regard, is it
> > > reasonable enough to use ordered.xtc for msd calculation?
> > >
> > > Please reply.
> > > --
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> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> >
> >
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.