Dear users, I am attempting to determine the free energy of self solvation of several small molecules. Starting with an equilibrated box of pure fluid (for example, ethanol - which I am calling thr) I am renaming all of the molecules except for the first in the .gro file SOL, then updating the .top file [ molecules ] section.
The free energy section of my .mdp file looks like this (this is mdout.mdp produced by grompp): ; Free energy variables free-energy = yes couple-moltype = thr couple-lambda0 = vdw-q couple-lambda1 = none couple-intramol = no init-lambda = -1 init-lambda-state = 15 delta-lambda = 0 nstdhdl = 200 fep-lambdas = mass-lambdas = coul-lambdas = 0.0 0.3 0.4 0.6 0.8 1.0 1.0 1.0 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 0.0 0.1 0.3 0.5 0.6 0.68 0.76 0.82 0.86 0.92 1.0 bonded-lambdas = restraint-lambdas = temperature-lambdas = calc-lambda-neighbors = -1 init-lambda-weights = dhdl-print-energy = yes sc-alpha = 0.001 sc-power = 1 sc-r-power = 48 sc-sigma = 0.3 sc-coul = no separate-dhdl-file = yes dhdl-derivatives = yes dh_hist_size = 0 dh_hist_spacing = 0.1 The issue is that the simulation appears to be coupling all of the molecules in the system, rather than just the single molecule named thr. In the log file produced by mdrun I get this line 'There are 2511 atoms and 2511 charges for free energy perturbation', when I am expecting there to be 9 atoms. Any ideas as to what could be causing all of my molecules to couple instead of just a single molecule? Thank in advance for your assistance! Brittany -- 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
