Thanks, Justin. I'll do experiments on that. Thu, 7/7/11, Justin A. Lemkul <[email protected]> wrote:
From: Justin A. Lemkul <[email protected]> Subject: Re: [gmx-users] placing dihedral constraints To: "Discussion list for GROMACS users" <[email protected]> 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. -Justin > 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 > > -----Inline Attachment Follows----- > > -- gmx-users mailing list [email protected] > <http://us.mc1615.mail.yahoo.com/mc/[email protected]> > 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 [email protected] > ><http://us.mc1615.mail.yahoo.com/mc/[email protected]>. > 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 ======================================== -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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