Dear All I want to calculate protein-drug binding free energy. I read Dr.Mobley tutorial(about free energy of methan dissapearing from water).I couldn't understand some of it's parts.
Can I use thisr tutorial in this case(protein-drug)? Besides, I have a few question about that: 1-What do I need to use as my .top & .gro files in my commands?(with regarding my problem)docked state or separated state?for example he has used methan(separated from water). 2-Are these files(.top & .gro) the same for all values of lambda? 3-Do these files(.top & .gro)change if you inversed the meaning of lambda=1 & lambda=0? 4-How did he define for (with which parameters) Gromacs that lambda=1 is relating to completely interacting & lambda=0 is relating to methan disappearing system? Please let me know the answer of my questions Thank in advance for your reply Sincerely yours Mohsen
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
