[gmx-developers] Problem with dihedral restraint in gromacs 4.6
landry.charlier at univ-montp1.fr
Mon Feb 11 16:05:34 CET 2013
Last question (I hope).
How can I choose the force constant?
Indeed for the version 4.5, the force constant is defined by the
option dihre_fc in the mdp input file. After this force is multiply by
kfac contained in the dihedral_sections in the topology file
Now this option is obsolete. The force constant is defined by kfac in
gromacs4.6 ? If yes, kfac has now a unit. In kJ.mol-1.rad-2 ?
Quoting Landry Charlier <landry.charlier at univ-montp1.fr>:
> OK, thanks for the reply.
> I have put a #ifdef DIH_RESTR in the topol file and define =
> -DDIH_RESTR in the mdp input file in order turn on the dihedral
> restraints. So I have not to erase the dihedral_restraints section
> in order to turn them off.
> Quoting "Shirts, Michael (mrs5pt)" <mrs5pt at eservices.virginia.edu>:
>> 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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