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 -- ================================================== 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
