On 4/27/15 1:29 AM, nao.morish...@takeda.com wrote:
Dear Gromacs Users, I would appreciate you to give me any comments or hints about the question below. What makes the calculation time much longer when I calculate a solvation free energy using the mdp input1 compared to the mdp input2? Input1 Free_energy = yes Couple-lambda0 = vdw-q Couple-lambda1 = none Couple-intramol = no Init-lambda-state = 2 Fep-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 Calc-lambda-neighbors = 1 Input2 Free_energy = yes Couple-lambda0 = vdw-q Couple-lambda1 = none Couple-intramol = no Init-lambda-state = 2 Fep-lambdas = 0.0 0.1 0.2 Calc-lambda-neighbors = 1 It takes three times longer when I write down 36 lambda values compared to 3 lambda values even if there is no difference between mdp inputs other than the value of fep-lambdas and it is a normal free energy calculation not like Hamiltonian replica exchange calculation.
In the second case, you're only evaluating the Hamiltonian at the native lambda and one other value (as there is only one neighbor). In the first case, you've got two neighbors. That doesn't explain the big difference in performance. Everything else about the run is the same - hardware, number of cores, etc?
Note that without couple-moltype, you're going to be decoupling the whole system, which is (1) not what you want for calculating solvation free energy and (2) extremely slow. There is an inherent slowdown when running the free energy code, but it should not be so large.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.
