[gmx-users] All molecules being coupled for free energy of self solvation simulation

[Brittany Zimmerman]

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