[gmx-users] Distance between centers of mass

[Justin Lemkul]

On 3/3/17 5:38 AM, CROUZY Serge 119222 wrote:
> 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 ?
>

Without seeing the actual output, screen output of grompp regarding the 
restraint length, etc. there's no way to say anything.

-Justin

> Thx
>
> -----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
>
>
>
> 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
>
> --
> ==================================================
>
> 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

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