[gmx-users] periodicity in msd calculation

[Bala subramanian]

Hi justin,
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
starting.

Thanks
Bala



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
>> (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.
>>
>
> http://lists.gromacs.org/pipermail/gmx-users/2010-July/052512.html
>
>
> -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