[gmx-users] Distance between centers of mass

CROUZY Serge 119222 serge.crouzy at cea.fr
Fri Mar 3 11:38:37 CET 2017

Hi  Justin 

Bouncing back on  your early answer about gmx distance, I noticed something strange (to me)

I'musing the same instruction for a protein file prot.gro
gmx distance ... -select "com of group 'Protein' plus com of group 'Ligand'"

and now I'm running umbrella sampling with pull code  starting from prot.gro
pulling groups are the same 'Protein' and 'Ligand'
and strange the first line in the pullx.xvg file does not give the same distance as gmx distance !!
Any idea why ?

-----Message d'origine-----
De : gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] De la part de Justin Lemkul
Envoyé : jeudi 2 mars 2017 23:12
À : gmx-users at gromacs.org
Objet : Re: [gmx-users] Distance between centers of mass

> 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 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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