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Bug #1002

g_dist lists ndx input as optional but fails if no index file provided

Added by Peter Kasson about 7 years ago. Updated over 6 years ago.

Status:
Closed
Priority:
Normal
Assignee:
-
Category:
-
Target version:
Affected version - extra info:
4.6, 4.5.x
Affected version:
Difficulty:
uncategorized
Close

Description

We should either make the index file required or (better yet) offer the default index groups.

Option Filename Type Description
------------------------------------------------------------
-f run_start2.gro Input Trajectory: xtc trr trj gro g96 pdb cpt
-s run.tpr Input Run input file: tpr tpb tpa
-n index.ndx Input, Opt. Index file
-o dist.xvg Output, Opt. xvgr/xmgr file
-lt lifetime.xvg Output, Opt. xvgr/xmgr file

Option Type Value Description
------------------------------------------------------
h bool no Print help info and quit
[no]version bool no Print version info and quit
nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
[no]intra bool yes Calculate distances without considering periodic
boundaries, e.g. intramolecular.
-dist real 0 Print all atoms in group 2 closer than dist to
the center of mass of group 1

Reading file run.tpr, VERSION 4.0.99_development_20090520 (single precision)

-------------------------------------------------------
Program g_dist, VERSION 4.6-dev-20120910-68140ec
Source code file: /Users/kasson/Desktop/Software/gromacs-4.6/src/gmxlib/futil.c, line: 531

File input/output error:
index.ndx
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Associated revisions

Revision d5856471 (diff)
Added by Alexey Shvetsov almost 7 years ago

[tools] Allow g_dist to use default index group

This should fix #1002

Change-Id: I93db5821bd2eb333f89c21d84f8f52eabc2a7dc3
Signed-off-by: Alexey Shvetsov <>

History

#1 Updated by Roland Schulz almost 7 years ago

  • Status changed from New to In Progress

#2 Updated by Erik Lindahl over 6 years ago

  • Status changed from In Progress to Closed

Fixed in revision d5856471.

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