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

Landry Charlier landry.charlier at univ-montp1.fr
Mon Feb 11 16:07:07 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Now this option is obsolete.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 ?

Thank you

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!
> Best,
> ~~~~~~~~~~~~
> Michael Shirts
> Assistant Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434)-243-1821
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