Project

General

Profile

Bug #84

g_order tool does not produce deut. order parameters

Added by Arneh Babakhani over 13 years ago. Updated over 13 years ago.

Status:
Closed
Priority:
High
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

This problem was first noted by Sukit Leekumjorn <> , as
described in his/her posting to the GMX user-list:

"I have encounter some problem with g_order in Gromacs3.3.1. I noticed that
tetrahedral order parameter has been added to the new version and for some
reason, the program seems to call for calc_tetra_order_parm loop rather than
calculate regular tail order parameter. For Gromacs3.3, the order parameter
calculates normally. Below is the run from g_order in 3.3.1. It stops at
"Select a group" and nothing proceed afterward when it should have picked the
listed atoms (group 0 to 17) and started the calculation. I did put group 0 and
the program started to calculate and it gave sg-ang.xvg and sk-dist.xvg as the
outputs. " (it does not give an output for the deuterium order parameters)

Prof. Van Der Spoel then suggested to remedy the problem by replacing (at lines
579 and 580, of gmx_order.c) the calls to opt2fn by opt2fn_null.

But even after doing this, recompiling and reinstalling GROMACS, the problem
persists (no change).

Thanks,

Arneh Babakhani

gmx_order.patch (1.62 KB) gmx_order.patch patch to gmx_order.c David van der Spoel, 06/03/2006 11:56 AM
gmx_order.patch-3.1.1 (1.81 KB) gmx_order.patch-3.1.1 gmx_order.c patch against gromacs-3.3.1 Paul van, 06/04/2006 11:10 AM

History

#1 Updated by David van der Spoel over 13 years ago

Created an attachment (id=42)
patch to gmx_order.c

his fix by Paul van Maaren might do the trick

#2 Updated by Paul van over 13 years ago

Created an attachment (id=43)
gmx_order.c patch against gromacs-3.3.1

The previous patch was against CVS release-3-3-patches, this one is against
gromacs-3.3.1.tgz from www.gromacs.org

#3 Updated by Arneh Babakhani over 13 years ago

Yep, this patch seems to do the trick, thanks!

(In reply to comment #2)

Created an attachment (id=43) [edit]
gmx_order.c patch against gromacs-3.3.1

The previous patch was against CVS release-3-3-patches, this one is against
gromacs-3.3.1.tgz from www.gromacs.org

Also available in: Atom PDF