Re: Free Energy Pertubation simulation set-up

Date: Sun Dec 06 2020 - 23:33:51 CST

An FEP setup is an protocol of TI , this have same steps that an clasical md simulation with diference in production. Where you need activate (NpT esemble) Alchm function into NAMD , type of decoupling, generaly using vdW-coulubm and choise lambda between 0-1 with equidistan lambda 0.05 for example for genérate windows.

For other Hand, yes as in tutorial from NAMD you need sepárate complex and run independient md.



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> El 6 dic. 2020, a la(s) 7:21 p. m., alli suliat <> escribió:
> Dear NAMD Users,
> I'm interested in obtaining in-silico binding affinities of some protein-ligand complexes by using NAMD. I've looked over the alchemical free energy perturbation tutorials with NAMD. However, I do not understand how the simulation process works or how to set-up my system for the FEP simulation.
> 1) One has to set-up two separate systems of; A (protein plus ligand) and B (ligand only)?
> 2) Can a previously minimized and equilibrated system be used for the simulations?
> 3) How long should the FEP simulation be?
> 4) How is the lambda state in the configuration file determined?
> Thank you.
> Sincerely,
> Adeola Alli

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