[gmx-users] g_msd for many molecules

[George Patargias]

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