[gmx-users] G_gyrate doubt

Justin A. Lemkul jalemkul at vt.edu
Sat May 1 02:29:28 CEST 2010

Maurício Menegatti Rigo wrote:
> Hi,
> we are working with a protein-ligand system (MHC + peptide). We have 
> computed radius of gyration using the following command line:
> g_gyrate -f File1.xtc -s File2.tpr -n index.ndx -o GYRATE
>       * File1: refer to concatenated trajectories of our *protein* plus 
> *ligand *during 8ns simulation.
> We choose the *ligand* group to compute the radius of gyration. My 
> questions are:
> 1) Which center of mass GROMACS will set: the center of mass of the 
> ligand or of the protein?
> 2) If the center of mass is the protein, all the atoms of the ligand are 
> used for the radius og gyration calculation?

I see no reason why the receptor's coordinates would be used if you tell 
g_gyrate to do its calculation on the peptide ligand.  If it did, I would think 
that would be a major flaw.

You can convince yourself of this fact by running g_gyrate on a single .gro file 
(extracted from the trajectory) that contains only the peptide (so that no other 
atoms can possibly be considered), and compare its results to that frame in the 
trajectory output.


> Thanks in advance
> -- 
> Maurício Menegatti Rigo
> Núcleo de Bioinformática do Laboratório de Imunogenética
> Departamento de Genética
> Instituto de Biociências
> Universidade Federal do Rio Grande do Sul


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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