[gmx-users] Problems with Jacobi diagonalization

[Mark Abraham]

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