[gmx-users] Radius of gyration

[Justin Lemkul]

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.

-Justin

> 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
>>
>> --
>> ==================================================
>>
>> 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
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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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
http://mackerell.umaryland.edu/~jalemkul

==================================================