[gmx-users] Eigenvalues not saved from gmx covar in GROMACS 5

Justin Lemkul jalemkul at vt.edu
Fri Aug 8 16:48:55 CEST 2014

On 8/7/14, 2:00 PM, Steven Morgan wrote:
> I have installed v5 of GROMACS and am doing simulations on a peptide VPGVG repeated five times.  I am trying to calculate entropy and the eigenvalues of the covariance matrix to get eigenfrequencies.  When I issue the command gmx covar -f full.trr -s full.tpr -v -o -mwa (for eigenvalues), I get an empty eigenvalues.xvg.  In GROMACS v4.5.5 I used to get the eigenvalues outputted, for the same data sets, same command (g_covar).  It says it's writing the eigenvalues, but when I open the file there are no eigenvalues there, only the preamble for the xvg file, ending at @TYPE xy.  What am I doing wrong or is this a bug?

Sounds like a bug.  Please file an issue on redmine.gromacs.org and upload 
example input files that reproduce the problem.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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