Mr Bernard Ramos wrote:
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
Increase kfac or dihre_fc. Probably the initial geometry doesn't like the
restraint being placed there so you may have to increase the energy penalty for
deviating from the restrained value.
from the original settings. Your help is greatly appreciated.
One more question. This restraining will not affect the final potential
energy right?
Certainly it will. You'd be preventing (or at the very least, disfavoring) EM
from adjusting surrounding coordinates. Such a procedure may have a positive or
negative outcome on the final energy.
-Justin
Bernard
--- On *Mon, 6/27/11, Mark Abraham /<mark.abra...@anu.edu.au>/* wrote:
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] placing dihedral constraints
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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