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Bug #1678

Duplicate Force Field Parameters?

Added by Michael Shirts about 5 years ago. Updated about 2 years ago.

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

In at least one file (opls.ff/ffbonded.itp), in version 5.0 (probably earlier) the same parameters are defined multiple times. For example, the line:

H N2 CA X 3 8.49352 0.00000 -8.49352 0.00000 0.00000 0.00000 ; aniline-like

Occurs on line:

opls.ff/ffbonded.itp:1935

and again on

opls.ff/ffbonded.itp:2385

There appear to be about 90 of these in this file.

It's not clear that its affecting any results (if gromacs pics the last one, for example, it's irrelevant) but it does seem like a poor choice to have multiple lines that have the same information in them. For example, if someone changed one of these lines, then the result might not match the changed result, because gromacs might process the other of the duplicated lines.

I won't paste the full list here, but it can be found with an file with

file.itp | uniq -c | more | sort | tail -N

Where N is some number larger than the number of suspected duplicated lines

Associated revisions

Revision e21fd969 (diff)
Added by Erik Lindahl about 2 years ago

Remove duplicated lines from OPLS ffbonded.itp

Only identical lines have been removed, as identified
with sort ffbonded.itp | uniq -c | sort.

Fixes #1678.

Change-Id: Id6f2b335f385ed31ddec1662d2f446b139067d1a

History

#1 Updated by Berk Hess over 4 years ago

Multiple copies with identical parameters lead to only a single entry being stored.
Multiple copies with different parameters leads to warnings in grompp and a fatal error, unless the user sets -maxwarn.
So technically this is harmless, but I agree this should be fixed.

#2 Updated by Berk Hess over 4 years ago

  • Status changed from New to Accepted

#3 Updated by Gerrit Code Review Bot about 2 years ago

Gerrit received a related patchset '1' for Issue #1678.
Uploader: Erik Lindahl ()
Change-Id: gromacs~release-2018~Id6f2b335f385ed31ddec1662d2f446b139067d1a
Gerrit URL: https://gerrit.gromacs.org/7327

#4 Updated by Erik Lindahl about 2 years ago

  • Status changed from Accepted to Fix uploaded

#5 Updated by Erik Lindahl about 2 years ago

  • Status changed from Fix uploaded to Resolved

#6 Updated by Erik Lindahl about 2 years ago

  • Status changed from Resolved to Closed

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