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 could do it in a stepwise fashion, varying the .top file only for
successive restarts, rather than tweaking with the C code.
Mark
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