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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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