[gmx-developers] question about repeated dihedraltyeps

Shirts, Michael R. (mrs5pt) mrs5pt at eservices.virginia.edu
Wed May 7 05:11:38 CEST 2014

Yea, that's the point.  I want to do several proper dihedrals (using 9), but grompp tells me that to have multiple ones, I should use type 4 -- which is an improper dihedral type (though its mostly bookkeeping, as the functional form is the same as 1 or 9).

Note that multiple dihedrals of type 9 are OK, but not multiple dihedral types.

Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu

From: Roland Schulz <roland at utk.edu<mailto:roland at utk.edu>>
Date: Tuesday, May 6, 2014 at 10:53 PM
To: "gmx-developers at gromacs.org<mailto:gmx-developers at gromacs.org>" <gmx-developers at gromacs.org<mailto:gmx-developers at gromacs.org>>, "michael.shirts at virginia.edu<mailto:michael.shirts at virginia.edu>" <michael.shirts at virginia.edu<mailto:michael.shirts at virginia.edu>>
Subject: Re: [gmx-developers] question about repeated dihedraltyeps

Are you trying to do several improper dihedrals? I don't think this is implemented. Type 9 is for several proper ones (for charmm force field).


On Tue, May 6, 2014 at 10:02 PM, Shirts, Michael R. (mrs5pt) <mrs5pt at eservices.virginia.edu<mailto:mrs5pt at eservices.virginia.edu>> wrote:

"Type 9 allows multiple potential functions to be applied automatically to
a single dihedral
in the [ dihedral ] section when multiple parameters are defined for the
same atomtypes in
the [ dihedraltypes ] section."

However, when I try this, grompp says:

"Overriding Proper Dih. parameters.
  Use dihedraltype 4 to allow several multiplicity terms.

  old: 0 1 3 0 1 3
  new: HC     CT     CT     HC      9     0   5 4

Should the code be checking for type 9, not type 4, since type 4 are
explicitly improper dihedrals?

Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu<mailto:michael.shirts at virginia.edu>

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