[gmx-users] Radius of gyration

[Parvez Mh]

Dr. Lemkul ,

thanks a lot. This really helped me .   I used cluster option    in -pbc
and this seems, put whole cluster in together. I am confused with , the
description of manual that, 'Note also that if your molecules are broken
this will not work either.'. As cluster is bigger and broken so it is
obvious that some molecules will be  broken. Is that mean, i can not use
cluster option in that case ?

Regards
Masrul

On Mon, Oct 19, 2015 at 7:21 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/19/15 8:12 PM, Parvez Mh wrote:
>
>> Dear All,
>>
>> In my simulation, a group of molecules form a big cluster. I want to
>> measure radius of gyration of this cluster. I know index of  molecules
>> those are part of the cluster. Problem  is, cluster is broken due
>> periodicity. Is it possible in gromacs, to measure radius of gyration of
>> this type of cluster?
>>
>>
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
>
> -Justin
>
> --
> ==================================================
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
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> University of Maryland, Baltimore
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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