[gmx-users] Wildcards and dihedral type 9

Mark Abraham Mark.Abraham at anu.edu.au
Fri Jan 27 10:59:29 CET 2012

On 27/01/2012 6:22 PM, Antila Hanne wrote:
> Dear experts,
> I'm a bit confused about the use wildcards in the dihedral definitions
> of .itp force field files. I'm under the impression that explicit
> definition of a dihedral (e.g. OS-CT-CT-OS) is always used if
> available and it overwrites any wildcards (for example X-CT-CT-X) that
> might match that particular dihedral. However:
> 1. Does the explicit definition replace wildcard if they have
> different periodicity. That is, are the expressions matched based on
> atom types alone or atom types and periodicity?

Don't know, but if you make a simple test case, you can use gmxdump to 
see what grompp decided to do. Note that the output of gmxdump starts 
numbering from zero, not one.

> 2. Does the use of dihedral type 9, which enables summation of several
> (type 1) dihedrals, have an effect on this?

I doubt it.


>   Thanks for the help!
>   Hanne Antila
>   Phd student
>   Aalto University
>   Finland--
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