[gmx-users] placing dihedral constraints
Mr Bernard Ramos
bgrquantum at yahoo.com
Wed Jul 6 19:29:50 CEST 2011
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?
--- On Mon, 6/27/11, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] placing dihedral constraints
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Monday, June 27, 2011, 5:38 PM
On 06/27/2011 07:31 PM, Mr Bernard Ramos wrote:
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].
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