Hello all, I am setting up a free energy calculation (drug from full coulomb+vdW in solution --> drug with only vdW in solution --> dummy drug in solution).
After reading most of the papers, I understand that you need significant overlap from the energies for each intermediate point to overlap so its best to have many intermediate points from Lambda=0 to Lambda=1. The drug molecule I have is a bit complex but I wasn't sure if using too small of an intermediate could have a bad effect on the free_energy calculation. I know Justin Lemkul said in its tutorial that Lambda=+0.05 should be good for most but I decided to go with Lambda=+0.02. Could this have any negative effect other than taking a longer time? Also, how does one come up with the best soft-core potential parameters to use? Is it ok to use the one from the Methane in water tutorial? Thanks for everyone's expertise. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: fabian.castebla...@gmail.com -- 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
