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Feature #2129

gmx mindist -or -respertime has an unmarked comment at the top of the .xvg

Added by Chris Neale almost 3 years ago. Updated almost 3 years ago.

Status:
Closed
Priority:
Low
Assignee:
-
Category:
analysis tools
Target version:
-
Difficulty:
uncategorized
Close

Description

In gmx 5.1.2, the command:

echo -e "r_1to20_AND_notH\nPOPC_POPS_AND_notH\n" | gmx mindist -s $tpr -f $xtc -n index.ndx -ng 1 -od mindistA.xvg -on contactsA.xvg -or mindistresA.xvg -group -d $CUTOFF -respertime -pbc

gives the following output in the mindistresA.xvg file:

# This file was created Thu Mar  2 11:49:45 2017
# Created by:
#                  :-) GROMACS - gmx mindist, VERSION 5.1.2 (-:
# 
# Executable:   /home/cneale/exec/GROMACS/exec/gromacs-5.1.2/serial/bin/gmx
# Data prefix:  /home/cneale/exec/GROMACS/exec/gromacs-5.1.2/serial
# Command line:
#   gmx mindist -s ../../../../../298K/tmp.tpr -f ../../../../tot_temp0.xtc -n index.ndx -ng 1 -od mindistA.xvg -on contactsA.xvg -or mindistresA.xvg -group -d 0.6 -respertime -pbc
# gmx mindist is part of G R O M A C S:
#
# Good ROcking Metal Altar for Chronical Sinners
#
@    title "Minimum Distance" 
@    xaxis  label "Time (ps)" 
@    yaxis  label "Distance (nm)" 
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "r_1to20_AND_notH-POPC_POPS_AND_notH" 
ACE0 LYS1 GLU2 

and the header line "ACE0 LYS1 GLU2" should be commented with '@' according to the pattern of other .xvg files.

Furthermore, if the -xvg none option is added, this header line is still printed to the output .xvg file.

Associated revisions

Revision e5242964 (diff)
Added by David van der Spoel almost 3 years ago

Removes rogue printing to xvg file in gmx mindist

-xvg none is now adhered to, and printing is preceded by
a comment.

Fixes #2129

Change-Id: Idf7135c7e74ea17747e0f5cacc9298a619e6c90d

History

#1 Updated by Gerrit Code Review Bot almost 3 years ago

Gerrit received a related patchset '1' for Issue #2129.
Uploader: David van der Spoel ()
Change-Id: gromacs~release-2016~Idf7135c7e74ea17747e0f5cacc9298a619e6c90d
Gerrit URL: https://gerrit.gromacs.org/6497

#2 Updated by David van der Spoel almost 3 years ago

  • Status changed from New to Fix uploaded

Fixed and merged.

#3 Updated by David van der Spoel almost 3 years ago

  • Status changed from Fix uploaded to Closed

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