[gmx-users] g_hbond error

[Erik Marklund]

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
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> 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
>


-- 
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys