Duplicate Force Field Parameters? - Redmine #1678
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
(from redmine: issue id 1678, created on 2015-01-25 by mrshirts, closed on 2017-12-11)
- Changesets:
- Revision e21fd969 by Erik Lindahl on 2017-12-11T20:53:38Z:
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