[gmx-users] periodicity in msd calculation

Justin Lemkul jalemkul at vt.edu
Tue Aug 21 16:09:14 CEST 2012

On 8/21/12 10:01 AM, Bala subramanian wrote:
> Friends,
> I have calculate the mean sq. displacement of water molecules in the first
> hydration shell around the protein (distance of .25nm). I want to write the
> code but i dnt know how to manipulate the coordinates to account for the
> pbc. Any guidance from anyone would be a great help.

Why not just run g_msd with an index file?  The closest water molecules can be 
reordered using trjorder.  Dynamic selections can be made with g_select, though 
those index groups cannot be used directly, but you can get something very close 
with trjorder + make_ndx.

Otherwise, see the existing code in g_msd for how it works.  It sounds like 
you'll be reusing most of its code anyway.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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