[gmx-developers] Small bug in current master

Justin Lemkul jalemkul at vt.edu
Sun Jun 21 18:03:10 CEST 2015

Hi Devs,

I stumbled across a very subtle bug when running gmx bar.  The title of the .xvg 
file causes read_xvg_legend() to report that there are no usable data in the file.

Compare this output from master (patched with Berk's intermolecular bondeds code):

# This file was created Fri Jun 19 23:49:56 2015
# Created by:
#      :-) GROMACS - gmx mdrun, VERSION 5.1-beta1-dev-20150616-bed7a9d (-:

# Executable:   /home/jalemkul/software/gromacs/git-master-intermol/bin/gmx
# Data prefix:  /home/jalemkul/software/gromacs/git-master-intermol
# Command line:
#   gmx mdrun -deffnm prod_fep_0 -px pullx_prod_fep_0.xvg -pf 
pullf_prod_fep_0.xvg -c safab1_prod_0.pdb -nt 16 -ntmpi 1 -ntomp 16
# gmx mdrun is part of G R O M A C S:
# GROningen MAchine for Chemical Simulation

with this one from 5.0:

# This file was created Sun Jun 21 10:59:51 2015
# Created by:
# GROMACS:      gmx mdrun, VERSION 5.0
# Executable:   /opt/mackerell/apps/gromacs/5.0.0/bin/gmx
# Library dir:  /opt/mackerell/apps/gromacs/5.0.0/share/gromacs/top
# Command line:
#   gmx mdrun -deffnm prod_fep_0 -c safab1_prod_0.pdb -pf pullf_0.xvg -px 
pullx_0.xvg -nt 16 -ntmpi 1 -ntomp 16
# gmx is part of G R O M A C S:
# Georgetown Riga Oslo Madrid Amsterdam Chisinau Stockholm

The blank line after

#      :-) GROMACS - gmx mdrun, VERSION 5.1-beta1-dev-20150616-bed7a9d (-:

causes parsing to fail and render gmx bar unable to find the data.  Adding a # 
to that line or removing it allows the program to run.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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