Thanks, Mark- I re-ran a short MD simulation with TDR as the only xtc group, and used tpbconv to create a .tpr file with only TDR (tpxout.tpr) and ran g_covar with an index.ndx that contains only TPR (just to be safe!),
g_covar -f traj.xtc -s tpxout.tpr -ref -n index.ndx and I still get the Jacobi error: Choose a group for the least squares fit Group 0 ( TDR) has 29 elements There is one group in the index Choose a group for the covariance analysis Group 0 ( TDR) has 29 elements There is one group in the index Calculating the average structure ... Reading frame 0 time 0.000 ------------------------------------------------------- Program g_covar, VERSION 3.3.3 Source code file: nrjac.c, line: 129 Fatal error: Error: Too many iterations in routine JACOBI ~Dayle On Wed, Apr 1, 2009 at 6:22 PM, Mark Abraham <[email protected]>wrote: > Justin A. Lemkul wrote: > >> >> >> Dayle Smith wrote: >> >>> Thanks for your help, Justin. I ran gmxcheck -c topol.tpr ("12284 atoms >>> in file") and gmxcheck -f traj.xtc ("# Atoms 29"). The difference is >>> >> >> Indeed, that's the problem, then! >> >> the SOL atoms. I made another .tpr file with xtcgroups = TDR SOL, and now >>> gmxcheck shows that the number of atoms in topol.tpr is 12284, but I still >>> can't get g_covar to work. Maybe these are unrelated problems, I'm not sure. >>> >> >> You haven't really changed anything. The xtc-grps parameter defines what >> was saved in the simulation. Setting it after the fact does not affect the >> already-produced .xtc file. What you need is a .tpr file that contains only >> TDR, so you would have to make modifications to your .top in order to >> generate this TDR-only .tpr file. >> > > Or use tpbconv - this is the "other" application for that utility. > > Mark > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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