[gmx-users] g_hbond error

[Justin A. Lemkul]

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.

-Justin

> Thanks
> Krishna
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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