[gmx-users] placing dihedral constraints

Mr Bernard Ramos bgrquantum at yahoo.com
Wed Jul 6 19:43:23 CEST 2011

Thanks, Justin. I'll do experiments on that. 
 Thu, 7/7/11, Justin A. Lemkul <jalemkul at vt.edu> wrote:

From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] placing dihedral constraints
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Thursday, July 7, 2011, 1:32 AM

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.


> Bernard
> --- 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:
>>     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
>     -----Inline Attachment Follows-----
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-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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