From: ROPÓN-PALACIOS G. (biodano.geo_at_gmail.com)
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.
Best.
Geordano.
Enviado desde mi iPhone
> El 6 dic. 2020, a la(s) 7:21 p. m., alli suliat <alliadeola17_at_gmail.com> 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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