[gmx-users] Problems with Jacobi diagonalization
Mark.Abraham at anu.edu.au
Thu Apr 2 03:22:15 CEST 2009
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.
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