[gmx-users] periodicity in msd calculation
bala.biophysics at gmail.com
Sat Sep 1 17:04:39 CEST 2012
Thanks and sorry for the delayed response.
I understand from the link that g_msd choose multiple restarts in a
given traj and averages the msd from the restart point to the end of
the trajectory. I would like to know if i can avoid such restart
points. I would like to choose one starting point as the reference and
calculate the msd of each succeeding points with respect to the
On Wed, Aug 22, 2012 at 6:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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
> 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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