Dear Colleagues,
I would like to perform MM/GBSA for a protein-ligand complex after minimization with an implicit solvent. In this regards, I have several questions:
1) What kind of radii is better to use for this task and is there any minimal recommended cutoff for implicit solvent simulations?
2) What should be the ratio of steepest descent and conjugate gradient cycles (maxcy, ncyc)?
3) I noticed that it is recommended to perform the minimization on CPU, what kind of consequences can have minimization on GPU with pmemd.cuda
Best regards,
Harut
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Received on Thu Oct 29 2020 - 13:00:02 PDT
