[gmx-users] placing dihedral constraints

[Justin A. Lemkul]

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.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-----
> 
>     -- 
>     gmx-users mailing list    gmx-users at gromacs.org
>     <http://us.mc1615.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use the
>     www interface or send it to gmx-users-request at gromacs.org
>     <http://us.mc1615.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 

-- 
========================================

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

========================================