[gmx-users] periodicity in msd calculation

Justin Lemkul jalemkul at vt.edu
Wed Aug 22 18:16:27 CEST 2012

On 8/22/12 12:12 PM, Bala subramanian wrote:
> 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
> coordinates.




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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