Hi all, I am using Gromacs4.5 for free energy calculations. At the beginning 6 lambda (0, 0.2, 0.4, 0.6, 0.8, 1.0) are used to test my system. There are two problems:
1. dV/dlambda value at lambda=0.0 is more than 300,000 KJ/mol, which is ten times large than those at the other lambda values (around 30,000 KJ/mol). All simulations at each lambda value are done during 100 ps. Since all the dV/dlambda is extremely large, I am wondering what it is related to. 2. Delta G value should be similar when the conformation is transfered from B state to A and in different sign. But integrations of all dV/dlambda are both positive in both cases (A to B, and B to A) in my results. I attach free energy stuff in the input file below. ; Free energy control stuff free_energy = yes init_lambda = 0.100 foreign_lambda = 0.1 couple-lambda0 = vdw-q couple-lambda1 = vdw couple-intramol = yes nstdhdl = 10 couple-moltype = system delta_lambda = 0 sc_alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 Thanks in advance, Jin -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
