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

[pratibha kapoor]

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.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>