[gmx-users] water dynamics

[pratibha kapoor]

Hello all

I have posted my query earlier but haven't got any reply and so re-posting
again:

I would like to monitor water dynamics in the protein's hydration layer eg.
calculation of mean square displacement, order parameter etc. In this
regard I have couple of questions:

I was going through the user list regarding calculation of mean square
displacement.  I believe while calculating msd, we should use the
trajectory as it is (without using pbc whole) and secondly removal of
center of mass of entire system is neccesary before calculating msd. These
are my parameters:
; mode for center of mass motion removal
comm-mode                = Linear
; number of steps for center of mass motion removal
nstcomm                  = 100
; group(s) for center of mass motion removal
comm-grps                =

Also, most of the simulations that deals with monitoring water dynamics are
carried out in NVT ensemble. But my simulations are in NPT ensemble.
So my question is
Can I proceed with g_msd command in NPT ensemble using above trajectory
(*.xtc file obtained directly after mdrun) and above center of mass removal
options (nstcomm not equal to 1) ?

Also, I would like to calculate msd of all non-exchangeable hydrogens. How
can I make index file containing these? Is there any better option than to
look at the *.gro file for hydrogens attached with atoms other than N and O
and manually add them one by one in index file?



On Wed, Aug 13, 2014 at 4:28 PM, pratibha kapoor <kapoorpratibha7 at gmail.com>
wrote:

> Hi everyone,
>
> I would like to monitor water dynamics in the protein's hydration layer
> eg. calculation of mean square displacement, order parameter etc. In this
> regard I have couple of questions:
>
> I was going through the user list regarding calculation of mean square
> displacement.  I believe while calculating msd, we should use the
> trajectory as it is (without using pbc whole) and secondly removal of
> center of mass of entire system is neccesary before calculating msd. These
> are my parameters:
> ; mode for center of mass motion removal
> comm-mode                = Linear
> ; number of steps for center of mass motion removal
> nstcomm                  = 100
> ; group(s) for center of mass motion removal
> comm-grps                =
>
> Also, most of the simulations that deals with monitoring water dynamics
> are carried out in NVT ensemble. But my simulations are in NPT ensemble.
> So my question is
> Can I proceed with g_msd command in NPT ensemble using above trajectory
> (*.xtc file obtained directly after mdrun) and above center of mass removal
> options (nstcomm not equal to 1) ?
>
> Also, I would like to calculate msd of all non-exchangeable hydrogens. How
> can I make index file containing these? Is there any better option than to
> look at the *.gro file for hydrogens attached with atoms other than N and O
> and manually add them one by one in index file?
>