[gmx-users] Time-dependent distance restraints

Oleg V. Stroganov stroganov at genebee.msu.ru
Tue Apr 5 17:58:40 CEST 2005

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 ..

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?

Best regards,

Oleg V. Stroganov, 
PhD student.

Moscow State University, 
Departments of Bioengineering and Bioinformatics. 
mailto:stroganov at genebee.msu.ru

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