Thanks Justin. Best regards, Fabian
On Mon, Aug 8, 2011 at 5:49 PM, Fabian Casteblanco <[email protected]> wrote: > 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: [email protected] > -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: [email protected] -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
