[gmx-users] g_msd for many molecules

[Florian Dommert]

Hi,

  if you want to calculate the MSD of several molecules, say nrmol, without using the
-mol option, which I do not know is still broken, you can do this in
three simple steps:

1. Convert your trajectory with trjconv and the option -pbc whole
2. Create an index file, that contains groups, which contain one
    molecule each, and remove the standard groups like System ...
3. run the analysis with: echo {0..nrmol} | g_msd -f convertedtrajecotry
-n indexfile -ng nrmol

This gives you the correct MSD for the center of mass for every
molecule.

Cheers,
Flo


* George Patargias <gpat at bioacademy.gr> [2013-05-02 10:08:20 +0300]:

>Thanks for this Vitaly and Justin.
>George
>
>> The resulting MSD will correspond to the average from individual atoms.
>>
>> Calculating MSD of an individual atom and ascribing it to a [small]
>> molecule, which this atom belongs to, is reasonable. Assuming that
>> averaged
>> MSD from atoms correspond to the cluster they form is not.
>>
>>
>> Dr. Vitaly Chaban
>>
>>
>>
>>
>> On Wed, May 1, 2013 at 2:40 PM, George Patargias <gpat at bioacademy.gr>
>> wrote:
>>
>>> Hello
>>>
>>> I am trying to calculate the MSD of 8 molecules in a lipid bilayer with
>>> g_msd. If I include the atoms of all these 8 molecules as a single group
>>> in the index file, will g_msd calculate the MSD of the center of mass of
>>> them or it will average over all atoms?
>>>
>>>
>>> Thanks
>>> George
>>>
>>>
>>> Dr. George Patargias
>>> Postdoctoral Researcher
>>> Biomedical Research Foundation
>>> Academy of Athens
>>> 4, Soranou Ephessiou
>>> 115 27
>>> Athens
>>> Greece
>>>
>>> Office: +302106597568
>>>
>>>
>>>
>>>
>>>
>>>
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>
>
>Dr. George Patargias
>Postdoctoral Researcher
>Biomedical Research Foundation
>Academy of Athens
>4, Soranou Ephessiou
>115 27
>Athens
>Greece
>
>Office: +302106597568
>
>-- 
>gmx-users mailing list    gmx-users at gromacs.org
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-- 
Dr.rer.nat. Florian Dommert

Institute for Computational Physics
University Stuttgart

Allmandring 3
70569 Stuttgart

EMail: dommert at icp.uni-stuttgart.de
Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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