[gmx-users] free energy calculations

[michael.b]

three questions regarding free energy calculations ...

1)  i try running a free energy calculation and get an error msg:

"The Verlet cut-off scheme does not (yet) support free-energy calculations
with perturbed atoms, only perturbed interactions. This will be implemented
soon. Use the group scheme for now."

in my top file i simply defined typeB, chargeB, massB for a particular
molecule,
my mdp file is below ... what is the difference between "perturbed
interactions" 
and "perturbed atoms"??

2) if i turn OFF a molecule turning all atoms in this molecule into dummy
types with zero charge
and vdw epsilon=0 ... do i have to explicitely tell gmx about the
bonded-interactions between
the various dummy atoms, or is gmx smart enough to simply use the original
parameters
from the un-perturbed molecule? does "couple-moltype" help here ??

3) is there anywhere such a thing as a tutorial for advanced free energy
methods,
in particular i'd be interested in trying expanded ensembles/hamiltonian
exchange ...

thanks!

michael




mdp file:

integrator               = sd
dt                       = 0.002
nsteps                   = 100000
comm-grps		 = System
;
nstxout                  = 100
nstvout                  = 0
nstfout                  = 0
nstlog                   = 100
nstenergy                = 100
;
nstlist                  = 20
ns_type                  = grid
pbc                      = xyz
cutoff-scheme            = Verlet
;
coulombtype              = PME
rcoulomb                 = 1.2
vdw_type                 = cut-off 
rvdw                     = 1.2
DispCorr                 = No
;
tc-grps                  = Other wat
tau_t                    = 0.2 0.2
ref_t                    = 298.0 298.0
;
gen-vel                  = yes
gen-temp                 = 40.0
gen-seed                 = 45411
continuation             = no
;
Pcoupl                   = berendsen 
Pcoupltype               = anisotropic
tau_p                    = 0.4 0.4 0.4 0.0 0.0 0.0
compressibility          = 1.0e-5 1.0e-5 1.0e-5 0.0 0.0 0.0
ref_p                    = 1.0 1.0 1.0 0.0 0.0 0.0
;
constraints              = h-bonds
constraint-algorithm     = LINCS
;
free-energy              = yes
init-lambda-state        = 0
delta-lambda             = 0
coul-lambdas             = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
vdw-lambdas              = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
calc-lambda-neighbors    = -1

sc-alpha                 = 0.002
sc-r-power               = 48
sc-coul                  = yes
sc-power                 = 1
sc-sigma                 = 0.3

nstdhdl                  = 100


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