[gmx-users] Distance between centers of mass

[Justin Lemkul]

On 3/2/17 4:15 PM, ÁLVARO RODRIGO RUIZ FERNÁNDEZ wrote:
> Dear GROMACS users:
>
> How can I calculate the distance between centers of mass of two residues in
> time with gmx distance?, I do not understand the  sentence "com of resname
> AAA plus com of resname BBB"  from the manual, pag 241 . Thanks.
>
>

This is simply the selection syntax for doing exactly what you describe.  You 
can select by residue name, number, etc. or by an existing index group, e.g.

gmx distance ... -select "com of group 'Protein' plus com of group 'Ligand'"

-Justin

-- 
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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

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