On 2/19/14, 1:05 PM, Jeff Chen wrote:
Dear All, I am trying to calculate the change in free energy that occurs when charging multiple type B molecules in an A-B mixture. For example, I have a mixture of 900 molecules of type A and 100 of type B. When coulomb interactions are on, B is identical to A (something like TIP4P water), but when coulomb interactions are off, each B is simply a Lennard-Jones particle (in the topology file, I've labelled B differently and called the molecule SOLB, but all interaction information is identical to A). To do the free energy calculations, I perform different simulations at each lambda point. For example, for a simulation with lambda=0, I have the following in my .mdp file: free_energy = yes init_lambda = 0.0 delta_lambda = 0 foreign_lambda= 0.05 couple-lambda0=vdw-q couple-lambda1=vdw couple-moltype=SOLB and when lamba=1, free_energy = yes init_lambda = 1.0 delta_lambda = 0 foreign_lambda= 0.95 couple-lambda0=vdw-q couple-lambda1=vdw couple-moltype=SOLB I expected that when lambda=0, B molecules would behave identically to A molecules with the coulombic energy fully turned on (couple-lambda0=vdw-q), and when lambda=1, B molecules would behave like LJ particles, with no coulombic interactions, either with each other, or with A molecules. However, when I look at the coulombic energy for B-B interactions (I used tpbconv -o to make a new *.tpr for only B molecules, then used mdrun -rerun with a trajectory containing only information about B molecules), I find that both the short-range and reciprocal coulombic energies are NOT zero as I had expected for lambda = 1, and are in fact exactly equal to the negative of the respective coulombic energies obtained using the same trajectory data when lambda=0.
What are the energies without using tpbconv and mdrun -rerun? In other words, it's necessary to figure out whether this is a problem in the original simulation with the free energy code (unlikely, given how simple the system is) or a problem using mdrun -rerun in conjunction with the free energy code (far more likely).
-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.
