[gmx-users] Radius of gyration
jalemkul at vt.edu
Wed Oct 21 03:48:12 CEST 2015
On 10/20/15 1:21 PM, Parvez Mh wrote:
> 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 ?
Molecules being "broken" across PBC and the cluster not being intact are
different concepts. The link I provided deals with this.
> 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
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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