[gmx-users] A bug of trjconv for force output?

Berk Hess gmx3 at hotmail.com
Wed Aug 13 09:18:03 CEST 2008


Indeed this is the problem.
I have fixed it in CVS for the Gromacs 4 release.

Thanks for reporting this bug,


> From: lulanyuan at msn.com
> To: gmx-users at gromacs.org
> Date: Tue, 12 Aug 2008 19:51:17 -0400
> Subject: [gmx-users] A bug of trjconv for force output?
> Hello All,
> I just found a strange problem for the gromacs tool trjconv. I have a trajectory (and the tpr file) which contains three groups of molecules and x,v and f. When I use trjconv to output the trajectory of the 1st group, everything is fine. For example, I have A,B and C groups in my trajectory and I choose A only at the prompt of trjconv and use "-force" option to include forces in my output trajectory of A only. But if I want a trajectory of C only, I found the output forces were wrong. Positions and velocities are right in this case. It seems to me the trjconv just pick the first N force numbers to write where N is the total number of atoms in group C. In fact these forces belong to group A and B. This "logic" of trjconv explains why the output is correct if I choose the first group A to write.
> Some month ago I reported a problem regarding the deshuf.ndx and the wrong force output. I think that problem is related to this problem. Because fewer people use forces, I think this is the reason these bugs haven't been found before. I appreciate if some authors can fix them.
> Thanks.
> Lanyuan Lu 
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