[gmx-users] Time-dependent distance restraints

David spoel at xray.bmc.uu.se
Tue Apr 5 20:17:37 CEST 2005

On Tue, 2005-04-05 at 19:58 +0400, Oleg V. Stroganov wrote:
> Hello Gromacs users,
> Does GROMACS allow to make time-dependent distance restraints? For
> example, I want my ligand to be slowly pulled from solution towards
> active site of enzyme, but unlike afm, I want restraining potential to
> be asymmetric (e.g. harmonic for the distances above 1 nm, and zero
> when ligand comes closer). I'm going to introduce [ distance_restraints ]
> section in my topology, but they appeared to be constant ..

What you want is not implemented in the normal distance restraints.
Maybe in the pull code. If you want to force the ligand to the active
site then you could consider using autodock or something like that.

> Is it possible to make r0 and r1 parameters of restraints change as the
> simulation goes on? Is it good idea to use topology A and B with
> different values of r0 and r1, and then simulate a kind of "Free
> Energy Perturbation" by conversion from state A to state B?
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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