I found the error, I had B states defined for my solvent molecules in the topology file.
On Wed, Aug 14, 2013 at 2:47 PM, Brittany Zimmerman <bsz...@virginia.edu>wrote: > 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
