[gmx-users] rephrase my question about torsional restraints

[David Mobley]

David,

Regarding the molecule merge, that makes sense.

However, should this work in the version (from Nov. 2004) that I have
to use for FEP/TI, or do I need the special version you're referring
to?

As far as perturbing the restraints is concerned, this is not a
problem: As long as I can adjust the spring constant, I can do the
"perturbation" that way: Simply modulate the spring constant manually
(in separate runs) to sample different values of the restraining
potential.

Thanks,
David


On 5/25/05, David <spoel at xray.bmc.uu.se> wrote:
> On Wed, 2005-05-25 at 09:19 -0700, David Mobley wrote:
> > David,
> >
> > Thanks for the response, but I'm not sure that this is a satisfactory solution:
> >
> > A) I need to do this in a free energy calculation, so I already have
> > to use the special CVS version (from Nov. 04) which includes the
> > reciprocal space part for the free energy calculations.
> > B) I don't actually want the two molecules to be connected -- I just
> > need to restrain relative orientations. From looking at the manual, it
> > looks like the -merge option joins the two molecules, which isn't what
> > I want (but perhaps I'm misunderstanding it?).
> You are, it doesn't connect the chains, just merges the two molecules
> into one molecule description which is necessary for technical reasons.
> >
> > To be a little more specific about what I'm trying to do, I'm doing
> > some FEP/TI for ligand binding where I first restrain the ligand
> > relative to some reference atoms in the protein (two angles, three
> > torsions, and a distance), and then turn off vdw and electrostatics.
> > I've done some calculations in AMBER, and am now trying to get the
> > same thing going in GROMACS.
> I'm not sure whether you can perturb dihedral restraints, the other
> things should work.
> 
> >
> > Let me know if this is currently not possible. I suppose another
> > option is that I simply restrain three different distances rather than
> > the six dof I'm currently doing, although this will require more
> > sampling.
> >
> > Thanks,
> > David
> >
> > On 5/25/05, David <spoel at xray.bmc.uu.se> wrote:
> > > On Wed, 2005-05-25 at 07:28 -0700, David Mobley wrote:
> > > > I wrote a question to the list several days ago about torsional
> > > > restraints (http://www.gromacs.org/pipermail/gmx-users/2005-May/015346.html),
> > > > and received no response, so let me rephrase:
> > > >
> > > > In Gromacs, is there a way (or what is the best way) to impose some
> > > > torsional restraints between several non-connected atoms -- i.e.,
> > > > between atoms AB in one molecule and BC in another molecule, to
> > > > restrain relative orientations of the two molecules? I also need to
> > > > know the contribution these restraints make to the energy.
> > > >
> > > > It is clear from the manual how to do this for distance restraints or
> > > > angle restraints, but not for torsions.
> > > You'll have to start with running pdb2gmx -merge on your two chains.
> > > Then you can restrain any four atoms
> > >
> > > [ dihedral_restraints ]
> > > i j k l type params
> > >
> > > It's only in CVS AFAIK.
> > > Try some params and check by running gmxcheck on your topol what you
> > > get.
> > >
> > > >
> > > > Thanks,
> > > > David Mobley
> > > > _______________________________________________
> > > > gmx-users mailing list
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> > > --
> > > David.
> > > ________________________________________________________________________
> > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > > Dept. of Cell and Molecular Biology, Uppsala University.
> > > Husargatan 3, Box 596,          75124 Uppsala, Sweden
> > > phone:  46 18 471 4205          fax: 46 18 511 755
> > > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > >
> > >
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
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