[gmx-users] rephrase my question about torsional restraints

[David]

On Wed, 2005-05-25 at 12:37 -0700, David Mobley wrote:
> 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?
No idea, please try it, or look up the gmx-revision mailing list
archives on the website, which documents changes in the CVS code.
> 
> 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
> > > > > gmx-users at gromacs.org
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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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-- 
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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