[gmx-users] periodicity in msd calculation
jalemkul at vt.edu
Tue Aug 21 16:09:14 CEST 2012
On 8/21/12 10:01 AM, Bala subramanian wrote:
> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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