[gmx-users] problem with dihedral restraints in gromacs 5.1.4.
mark.j.abraham at gmail.com
Fri Sep 15 10:55:06 CEST 2017
This approach to dihedral restraints was removed in 4.6, and removed from
the documentation in 5.0. In such versions, you need to implement such
restraints wholly in the topology file. See PDF reference manual for
On Fri, Sep 15, 2017 at 7:22 AM minky son <minky0710 at gmail.com> wrote:
> I have tried to introduce dihedral restraints in gromacs 5.1.4.
> I modified topology file and mdp file as following:
> In my topology file,
> #ifdef DIHRE
> [ dihedral_restraints ]
> ; ai aj ak al type phi dphi kfac
> 7 8 9 10 1 180 0 100
> 7 8 9 14 1 180 0 100
> 10 9 8 21 1 180 0 100
> 14 9 8 21 1 180 0 100
> In my mdp file,
> ;dihedral restraints
> dihre = simple
> dihre-fc = 100
> dihre-tau = 0
> nstdihreout = 50
> But the following outputs means restraints are not working.
> Ignoring obsolete mdp entry 'dihre'
> Ignoring obsolete mdp entry 'dihre-fc'
> Ignoring obsolete mdp entry 'dihre-tau'
> Ignoring obsolete mdp entry 'nstdihreout'
> No detailed information was found in the User's manual v.5.1.4.
> Also, I wonder if there is only an explanation of the old version on the
> web page (http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints
> Any idea on how to solve this problem could be of help.
> Thank you in advance,
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