Hi, Joakim- Expanded ensemble is still a bit experimental. I don't immediately see any problem that jump right out, but if you go to http://redmine.gromacs.org/ and file a bug report, including giving example files that cause the problem, I can take a look at it.
On Tue, Feb 5, 2013 at 6:00 AM, Joakim Jämbeck <jamb...@me.com> wrote: > 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 -- 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
