[gmx-users] periodicity in msd calculation

[Mark Abraham]

On 2/09/2012 1:04 AM, Bala subramanian wrote:
> 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.

  OK, so have a read of g_msd -h and choose what you want to do.

Mark

>
> 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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>
>