Hi Mark and everyone!
This has been a previous topic though and thanks Mark for the reply.
What I need to do is to calculate the potential energy (energy minimzation) of
a molecule at every fixed pairs of dihedrals (phi, psi). I did the suggestions
on http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints. In fact
what follows is the entry I placed in my topol.top
[ dihedral_restraints ]
; ai aj ak al type label phi dphi kfac power
5 1 40 38 1 1 30 0 1 2
12 40 38 34 1 1 10 0 1 2
I also added the following in my mdp file
dihre = yes
dihre_fc = 10000
I removed disre_tau and nstdihreout as they are no longer needed in the recent
gromacs versions. Unfortunately, after checking the dihedral angles, they
appear to be far from the set value of (phi=30, psi=10). I understand that we
are restraining the angles and not constraining/fixing them. Is there a way we
can have the resulting phi and psi as close to the required values? I get
values 15 degrees away from the original settings. Your help is greatly
appreciated.
One more question. This restraining will not affect the final potential energy
right?
Bernard
--- On Mon, 6/27/11, Mark Abraham <[email protected]> wrote:
From: Mark Abraham <[email protected]>
Subject: Re: [gmx-users] placing dihedral constraints
To: "Discussion list for GROMACS users" <[email protected]>
Date: Monday, June 27, 2011, 5:38 PM
On 06/27/2011 07:31 PM, Mr Bernard Ramos wrote:
Hi!
I would like to freeze two dihedrals/torsion angles but allow the rest (i.e.
bonds, angles) to relax during energy minimization and MD. How do I go over
applying constraints? Thanks.
See http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints
to sort out some nomenclature. You probably want a dihedral restraint with a
strong force constant (though other approaches are possible). See relevant
parts of chapters 4 and 5. Work by analogy from the [dihedrals] and
[position_restraints] sections in your existing [moleculetype].
Mark
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