[gmx-users] Mass Weighted Covariance matrix

Justin Lemkul jalemkul at vt.edu
Mon Aug 29 14:56:57 CEST 2016

On 8/29/16 12:16 AM, Tushar Modi wrote:
> Hello
> I am trying to calculate mass weighted covariance matrix using a Gromacs
> Topology file <tpr> and a trajectory file <xtc>. The trajectory has only
> protein coordinates.
>  I am using "gmx_mpi covar" function for the same. I am using following
> format from the documentation:
> gmx_mpi covar -f <traj> -s <topology> -ascii -mwa -b <> -e <>
> I have tried it both with and without mwa, but in both cases the log file
> generated says that the analysis is non mass weighted.
> Does that mean that the covariance matrix is also non mass weighted or not??

Are the covariances matrices generated with and without explicit mass weighting 
different?  This could just be a simple output bug and nothing in the actual 
calculation.  What version of GROMACS are you using?



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


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