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

[Brittany Zimmerman]

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 <bsz9ur at 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
>