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I'm working on translating some forcefield amino acid parameters to Q's format, but I have a question about one of the parameters used in the [torsions] section of the .prm file. According to the Qmanual, the 8th column is the "number of paths", which seems to be defined as:
is the number of ways that a two-atom torsion can be defined, i:e: the product of the number of atoms bonded to the two middle atoms. It is used to distribute the force over all the atoms involved.
Further, I can see that whenever wildcard atom flags are present, these values seem to be able to go higher than 1.0. However, for impropers where you have the 4 atom types defined, this variable always seem to default to 1.0, as seen here:
I then tried looking at the Fortran code to see how was this #paths variable used but I couldn't find it. Is this some sort of deprecated parameter? And is it fine if I would define a Amber-based forcefield using this #paths parameter as 1.0 for all the torsions defined?
The text was updated successfully, but these errors were encountered:
David-Araripe
changed the title
Unclear usage of number of paths
Question about number of paths parameter in Q's forcefield.prm definition
Jun 24, 2024
I'm working on translating some forcefield amino acid parameters to Q's format, but I have a question about one of the parameters used in the
[torsions]
section of the.prm
file. According to the Qmanual, the 8th column is the "number of paths", which seems to be defined as:However, this doesn't seem to match the values. I would understand it if all the carbon-carbon bonds would be defaulted to 9 but that doesn't seem to be the case as you can see here: https://github.com/qusers/Q6/blob/master/ff/amber14sb/qamber14.prm#L759-L762
Further, I can see that whenever wildcard atom flags are present, these values seem to be able to go higher than 1.0. However, for impropers where you have the 4 atom types defined, this variable always seem to default to 1.0, as seen here:
https://github.com/qusers/Q6/blob/master/ff/amber14sb/qamber14.prm#L856-L861
I was looking at the other forcefield definitions to understand this, but for OPLS2015 it seems to be always left as 1.0, as seen here:
https://github.com/qusers/Q6/blob/master/ff/oplsaam2015/qoplsaa.prm#L749-L767
I then tried looking at the Fortran code to see how was this
#paths
variable used but I couldn't find it. Is this some sort of deprecated parameter? And is it fine if I would define a Amber-based forcefield using this#paths
parameter as 1.0 for all thetorsions
defined?The text was updated successfully, but these errors were encountered: