Actually, I believe that using the energy difference, Delta E, as an approximation to the free energy difference, Delta G, is a valid approach (which I'm considering myself). The entropic contribution to Delta G, namely -T Delta S, may be less prominent than Delta E. In addition, Delta S can be approximated by various means - see e.g. Doig & Sternberg 1995. I understand that such an approach is utilized in the Accelrys Discovery Studio. Obviously, this is an approximation that might be too crude for some applications.
What do you think? ------------------------------------------------------------------------ -- On Oct 21, 2010, at 09:25 , Sander Pronk wrote: Hi Mohsen, The mean energy difference is only one component of the free energy difference. Before you go any further I'd suggest reading a good book on molecular simulations, like 'Understanding Molecular Simulations' by Frenkel and Smit. There's a good reason free energy calculations cover over half of that book. Sander On Oct 21, 2010, at 09:18 , mohsen ramezanpour wrote: > Dear Justin > > If I do two MD simulations for a short time in the same conditions(of course separately for protein and drug) > and calculate total energy of each one and sum them with each other as E1 as nonbonding free energy of system. > then a MD simulation for Protein-drug system in the same condition and calculate it's total energy too as E2 as bound system . > what does (E1-E2)mean? > I think it is binding free energy,Is not it? > in the other hand when we are working on NPT ensamble it means Gibbs free energy is the main energy and our total energy is equal to Gibbs free energy. > Then,what is the problem? -- 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
