On 2/20/14, 1:00 AM, Jeff Chen wrote:
Thank you very much for the quick reply. Without using tpbconv and mdrun -rerun, I'm not sure how to get the solute-solute energies from gromacs (please let me know it there's a way to do this) -- since there are many more solvent molecules, the total potential energy
Nonbonded interactions are decomposed with energygrps. If you didn't include that keyword and proper settings in the original run, then you need to use mdrun -rerun, but that doesn't really help for solving this issue. Investigating energygrps while the free energy code is on is worth checking into on its own. In principle, it should work, but may simply have never been tested.
is dominated by solvent-solvent and solvent-solute interactions. However, the total potential energy from a simulation (not a free energy simulation) with the solute charges set to zero is different than that obtained from a free energy simulation with lambda=1 -- the differences are fairly small, but big enough to be worrisome.
Good to know. What Gromacs version is this?
I'll run a system with fewer solvent molecules to get a better handle on what's going on -- thanks again for your suggestions. It seems most people do free energy calculations with a single solute molecule -- in your opinion, is it very unlikely that there is any problem in the way solute-solute interactions are handled in the free energy simulations?
That would be a fundamentally serious flaw in the free energy code; I think it highly unlikely that something so essential is broken.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
