Justin A. Lemkul skrev:


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

Agreed. That ought to work. I have an idea of what the problem might be, and it should be a fairly easy fix. Still, a bugzilla will prevent me or someone else from forgetting about it, so please submit one.

/Erik
Thanks
Krishna


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Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
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