[gmx-users] analyze diffusion of water in first hydration shell
kapoorpratibha7 at gmail.com
Mon Aug 18 11:31:39 CEST 2014
Thanks Tsjerk for clearing my doubt.
Is there any other inbuild function which can serve my purpose?
> 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?
> > guess this would serve the purpose and there is no need to specifically
> > n closest water in index group (Please correct me if I am wrong). But
> > what does following line mean (line copied from trjorder -h):
> > "When an index group of the first n waters is made, the ordered
> > 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
> > 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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