[gmx-users] Explicit Topology Question

Thomas Allen thomas.c.allen at rice.edu
Mon Jan 9 19:30:12 CET 2017

Hello all,

I'm currently implementing a simple polymer coarse-grained model in  
GROMACS through some modifications to the OPLS force field. An issue  
I'm having is that there are certain angles generated when parsing the  
topology file which I don't want. For example, assuming atoms A, B, C,  
I get the angles:

A B +C


-C B A

However, I only want the forward version (A B +C). I know that  
unwanted dihedrals can be excluded by topology file settings, and I  
know that CHARMM has settings which allow only certain angles or other  
interactions specified explicitly in the topology file entry to be  
generated for a given residue. I was wondering if there was an  
equivalent when using GROMACS, or if I will have to come up with some  
clever text editing to fix the issue in the topol.top file itself.

Tom Allen

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