[gmx-developers] Problem with dihedral restraint in gromacs 4.6
k.a.feenstra at vu.nl
Mon Feb 11 16:17:01 CET 2013
Could you please move this discussion to the users list?
This type of questions should be asked there.
On 11/02/13 16:07, Landry Charlier wrote:
> 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 Now this option is obsolete.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
>> 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
>> gmx-developers mailing list
>> gmx-developers at gromacs.org
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>> www interface or send it to gmx-developers-request at gromacs.org.
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