[gmx-users] Regarding msd

[rajat desikan]

Hi Justin,
I get identical results when I use g_msd (should have been clearer at the
outset). However, if I extract the coordinates from an unprocessed
trajectory with g_traj and run it in my own MSD code, I get different (and
wrong) results than if I use -pbc nojump (which ensures a continuous
trajectory). Since Pratibha wants to test her own code, the way she treats
pbc is something to keep in mind.

On Wed, Oct 8, 2014 at 4:59 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/8/14 3:21 AM, rajat desikan wrote:
>
>> Hi,
>> You need to use -pbc nojump to calculate the msd. Using -pbc whole is
>> wrong
>> for calculating the msd.
>>
>>
> Upon what do you base this statement?  I get identical results with an
> unprocessed trajectory, and those treated with either -pbc whole or -pbc
> nojump.
>
> -Justin
>
>  On Tuesday, October 7, 2014, pratibha kapoor <kapoorpratibha7 at gmail.com>
>> wrote:
>>
>>  Hi all
>>>
>>> I have created my own code for msd calculation and would like to verify
>>> it
>>> from g_msd. I have created pdb files using trjconv -center -pbc whole
>>> option. Can I use the coordinates in pdb as such (with no
>>> wrapping/unwrapping/shifting) for running my code? or does the inbuild
>>> g_msd program modifies them (shift)?
>>> My msd values are not matching with the g_msd values. I suspect that
>>> discrepency in the pdb file creation since the values obtained from my
>>> program agrees with manual calculation (of some dummy values).
>>> Any suggestions are highly welcomed.
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>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
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>
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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore