Re: [gmx-users] Eigenvalues not saved from gmx covar in GROMACS 5
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 -- == 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 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.
Re: [gmx-users] Eigenvalues not saved from gmx covar in GROMACS 5
Hi Steven, The eigenvalue is the variance of the projection over time. So in stead of waiting for the bug fix, you can also calculate the projections and get the eigenvalues from those. Hope it helps, Tsjerk On Aug 7, 2014 10:32 PM, Steven Morgan smor...@brooklyn.cuny.edu 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? Thank you, -Steven -- 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. -- 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.
[gmx-users] Eigenvalues not saved from gmx covar in GROMACS 5
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? Thank you, -Steven -- 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.
