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Bug #1118

trjconv won't output trr files

Added by Andy Somogyi over 4 years ago. Updated almost 4 years ago.

Status:
Closed
Priority:
Normal
Assignee:
-
Category:
-
Target version:
-
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

trjconv will not output trr files when using -sub index

Simple fix, change line 923 of gmx_trjconv.c from
if ((ftp != efXTC) && (ftp != efTRN))
to
if ((ftp != efXTC) && (ftp != efTRR))

With this change, trjconv seems to work fine when using -sub index.ndx and -o somefile.trr

Associated revisions

Revision 372187d7 (diff)
Added by Mark Abraham over 4 years ago

Fix trjconv -sub with .trr files

ftp is set from the -o file's extension, which cannot be efTRN,
since that's a place-holder file type for command-line parsing.
The error text clearly indicates that .trr (== efTRR) should
work, but of course we have no tests for anything.

Added comment that other trajectory types could work here,
but can't be tested at this time.

Fixes #1118

Change-Id: I118b9b1c25fa7c0640c27e584400dfc64853e67f

History

#1 Updated by Andy Somogyi over 4 years ago

Correction, with the above change, trjconv claims to output trr, however the resulting trr contains ALL atoms, not the subset specified in the sub.ndx.

In many cases, the velocities and forces are required, so xtc won't do, trr is required.

#2 Updated by Justin Lemkul over 4 years ago

Please state which version of Gromacs is affected. There was a fix for trjcov -sub merged into the git repo very recently (https://gerrit.gromacs.org/#/c/1463/) that does something different. It would be good to know whether or not this fixes your issue or whether we need to continue investigating it.

#3 Updated by Andy Somogyi over 4 years ago

All version affected, including current git / master.

#4 Updated by Andy Somogyi over 4 years ago

I'll try changing git / master gmx_trjconv.c to ((ftp != efXTC) && (ftp != efTRR)), to see if this change along with (https://gerrit.gromacs.org/#/c/1463/) does the trick.

#5 Updated by Mark Abraham over 4 years ago

  • Status changed from New to Accepted
  • Affected version set to 4.5.5

#6 Updated by Mark Abraham over 4 years ago

  • Status changed from Accepted to In Progress

#7 Updated by Mark Abraham over 4 years ago

  • Status changed from In Progress to Resolved

#8 Updated by Rossen Apostolov almost 4 years ago

  • Status changed from Resolved to Closed

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