[gmx-users] periodicity in msd calculation

Bala subramanian bala.biophysics at gmail.com
Wed Aug 22 18:12:36 CEST 2012

Hi justin,
Thanks for the suggestion. I will look at the code. Meanwhile I have
one doubt regarding the following option of the g_msd tool.

“-trestart    time   10      Time between restarting points in trajectory (ps)”
What does this -trestart indicates actually. I did a small trail run
on a 100ps trajectory (containing 500 snapshots) with snapshots
collected at .2ps interval. In the output file, it is printed as “#
MSD gathered over 100 ps with 11 restarts”.

Does it mean that the MSD is calculated with 11 different reference


On Tue, Aug 21, 2012 at 4:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
> --
> ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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C. Balasubramanian

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