[gmx-developers] Problem with dihedral restraint in gromacs 4.6

Shirts, Michael (mrs5pt) mrs5pt at eservices.virginia.edu
Mon Feb 11 15:42:21 CET 2013

Hi, all-

> Indeed, if i check the mdout.mdp file generated during the grompp
> step, there is no dihre option as in the version 4.5.
> So how can I turn on/off the dihedral restraints without the dihre option?

Using the topology, like you are doing now.

> For the moment, I modify the topology file by put or erase the
> dihedral_restraints section. The dihre option was more useful.

The goal of this change was to harmonize all of the free energy and A <-> B
state options; the mix of types resulted in bugs and complexity in the
underlying code.  Now, all types of transformation use the same syntax.  If
there are issues with the interface, please let us know!

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

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