Hi, I am trying to use the Expanded Ensemble (EE) method to compute the free energy of solvation of a small organic molecule.
Basically I am playing around but I cannot get the simulations to run. Here are my EE and free energy settings: %------------------------------------------------------- free-energy = expanded ; Expanded ensemble couple-moltype = C1X ; Molecule to introduce couple-lambda0 = none ; Go from no interactions with solvent... couple-lambda1 = vdw-q ; ...to full interactions couple-intramol = no ; Do not decouple internal interactions init_lambda_state = 0 ; Start from the first column of the lambda vectors delta-lambda = 0 ; No increments in lambda nstdhdl = 100 ; Frequency for writing dH/dlambda coul-lambdas = 0.0 0.25 0.5 0.75 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 vdw-lambdas = 0.0 0.0 0.0 0.0 0.0 0.2 0.4 0.6 0.7 0.8 0.9 1.0 dhdl-print-energy = yes ; Include total energy in the dhdl file sc-alpha = 0.5 ; Soft core alpha parameter sc-power = 1 ; Power of lambda in soft core function sc-r-power = 6 ; Power of radial term in the soft core function sc-sigma = 0.3 ; Soft core sigma sc-coul = no ; No soft core for Coulomb separate-dhdl-file = yes ; Seperate dhdl files dhdl-derivatives = yes ; Print derivatives of the Hamiltonian ; expanded ensemble variables nstexpanded = 100 ; Number of steps between attempts to change the Hamiltonian lmc-stats = wang-landau ; WL algorithm to explore state space lmc-move = gibbs ; Decides which state to move to lmc-weights-equil = number-steps ; EE weight updating stops after... weight-equil-number-steps = 5000000 ; ...10ns of simulation ; Seed for Monte Carlo in lambda space lmc-seed = 1993 lmc-repeats = 1 lmc-gibbsdelta = -1 lmc-forced-nstart = 0 symmetrized-transition-matrix = no nst-transition-matrix = -1 mininum-var-min = 100 wl-scale = 0.6 wl-ratio = 0.8 init-wl-delta = 1 wl-oneovert = yes %------------------------------------------------------- Besides this I use LINCS to constrain all bonds, sd-integrator and a "normal" cut-off scheme with a 1 fs time step. However, once I try to run the files on the cluster I always end up with LINCS warnings and after a few seconds the program crashes due to too many LINCS warnings. If I increase the time step to 2 fs I run into problems SETTLE for the water. I always start from a nice structure that is taken as the final snap shot from a simple 1 ns MD simulation of my system. What could be the problem? If I use free_energy = yes instead of EE things work fine. Did I perhaps mess up the EE settings or something? Thanks in advance. Best, Joakim -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
