Hi all, I want to calculate the free energy difference for ATP-->GTP in solution, for the forward analysis, the parameters for free energy perturbation are as follows: free-energy = yes sc-alpha = 0.3 sc-power = 1 sc-sigma = 0.25 sc-coul = no couple-intramol = yes init-lambda-state = $LAMBDA$ coul-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 vdw-lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0 nstdhdl = 50 calc-lambda-neighbors = 1
The calculated free energy difference is about -273 kJ/mol. In order to check the FEP convergence, backward analysis was also done. I adopt two ways to carry out backward analysis. (1) Modify the topology file for GTP--> ATP , the parameters of free energy calculation is the same as forward analysis. And the free energy difference of backward is about 213 kJ/mol. (2)Using the same topology file as forward analysis. But modify the parameter settings of coul-lambdas and vdw-lambdas for free energy calculation shown as follows free-energy = yes sc-alpha = 0.3 sc-power = 1 sc-sigma = 0.25 sc-coul = no couple-intramol = yes init-lambda-state = $LAMBDA$ coul-lambdas = 1.0 0.9 0.8 0.7 0.6 0.5 0.4 0.3 0.2 0.1 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.00 0.0 vdw-lambdas = 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 0.95 0.9 0.85 0.8 0.75 0.7 0.65 0.6 0.55 0.5 0.45 0.4 0.35 0.3 0.25 0.2 0.15 0.1 0.05 0.0 nstdhdl = 50 calc-lambda-neighbors = 1 The calculated free energy difference is about 272 kJ/mol Theoretically, the two ways of backward analysis is the same. And the values of free energy should be identical. Now, I am confused whether I misunderstand something or set the wrong parameters for FEP calculation. Would you like to give me some help? Thanks in advance. Best wishes Duan Baogen Beijing Computational Science Research Center -- 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.