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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phone: +46 18 471 4537 fax: +46 18 511 755
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