[gmx-users] Change restraints during md

David van der Spoel spoel at xray.bmc.uu.se
Tue Feb 28 13:16:17 CET 2006

Michal Kolinski wrote:
> Hello all.
> I wonder is there a way for turning off the distance restraints during 
> the md simulation.
> I’m currently investigation different binding modes of a small
> ligand inside the active site of the receptor protein. 
> I use restraints to force a proper orientation of ligand
> inside the active site during the first stages of the simulation.
> Then I would like to slowly turn off the restraints between protein and 
> small
> molecule (without a rapid change in distance restraints force) to
> investigate the complex stability. 
> Maybe someone knows how to implement
> it in Gromacs code?  Please give me some advice.

You want to modify the force constant from the initial value to zero, 
much like simulated annealing.

This is not implemented but could be done in md.c

the variable you want to change is inputrec->dr_fc

>  Thank you for help.
> Best wishes.
> Michal
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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://folding.bmc.uu.se

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