[gmx-users] analyze water in the hydration shell

[pratibha kapoor]

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.