|
Thank you for your advice. Yes, I thought about making series of runs with different forces for
restraints.
I wonder if restarting from trr files gives me perfect continuation
for the runs.
Michal
> 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 > 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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