Hello, everyone!
I'm a new user in gromacs, and now I have to perform a steered pulling code
on a ligand-receptor complex. The ligand is to be pulled away from the binding
site of the receptor, and umbrella sampling will be used to gain the PMF
(potential mean force) curve. Then binding energy of the ligand-receptor
complex would be estimated. The receptor contains 303 residues. While the
ligand is pulling away, the whole receptor is restrained by posres, 1000 in x,
y and z axis.
Since the receptor is so large and umbrella sampling needs so much
calculations, a very long time will be taken to complete the work.
Now I have my question, is there anyway to reduce the taken time? Such as
keeping only residues near the binding site to respect the whole receptor?
Thank you all in advance!
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