[gmx-users] Mass Weighted Covariance matrix

Tushar Modi Tushar.Modi at asu.edu
Mon Aug 29 06:17:41 CEST 2016


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??

With best Regards
Tushar Modi
Graduate Student
Department of Physics
Arizona State University

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