[gmx-users] Radius of gyration
parvezmh89 at gmail.com
Tue Oct 20 19:21:45 CEST 2015
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 ?
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?
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
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> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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