[gmx-users] analyze water in the hydration shell

pratibha kapoor kapoorpratibha7 at gmail.com
Sun Aug 17 11:20:28 CEST 2014

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.

More information about the gromacs.org_gmx-users mailing list