Duplicate Force Field Parameters?
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:
and again on
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
#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.