[gmx-users] g_hbond error

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 5 00:26:44 CEST 2009

krishnakumar wrote:
> Hi,
> Has any one encountered this error while using g_hbond?
> *********************************************************************
> Select a group: 12
> Selected 12: 'SOL'
> Select a group: 12
> Selected 12: 'SOL'
> Calculating hydrogen bonds in SOL (20949 atoms)
> -------------------------------------------------------
> Program g_hbond, VERSION 4.0.4
> Source code file: gmx_hbond.c, line: 565
> Fatal error:
> Error in func_type Position Rest.
> -------------------------------------------------------
> ************************************************************************
> I get this error only when using trajectory with positional restraint 
> during MD.
> Is there any fix for this bug?

Probably not, unless you submit a bugzilla :)  The search page is not working 
properly due to the website migration, so it might be hard to determine if 
anyone else has reported such a problem.  It may be due to the fact that typical 
use of position restraints is for equilibration, with the PR time period getting 
discarded (not analyzed).  Thus, you are doing an analysis that was unforeseen.

If you want to analyze this portion of the trajectory, you could create a new 
.tpr file (identical to your original, but without defining position restraints 
in the .mdp file), and trying to run the analysis again.  If that alleviates the 
problem, it would be useful to include as part of a bugzilla report.


> Thanks
> Krishna
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list