[gmx-users] analyze water in the hydration shell

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Aug 17 16:16:47 CEST 2014

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



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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