G_hyd using FEP with Gromacs

EM.mdp

; RUN CONTROL PARAMETERS = 
integrator               = steep
; start time and timestep in ps = 

; 6 ns.  This turns out to be long enough for systems without slow intramolecular degrees of freedom
nsteps               = 5000
emtol 		     = 100
emstep		     = 0.01	
; mode for center of mass motion removal = 

; We remove center of mass motion.  In periodic boundary conditions, the center of mass motion is spurious; the periodic system is the same in all translational directions.
comm-mode                = Linear
; number of steps for center of mass motion removal = 

; Output frequency for energies to log file and energy file = 
nstlog                   = 1
nstenergy                = 1

; NEIGHBORSEARCHING PARAMETERS = 
; nblist update frequency = 
nstlist                  = 1
; ns algorithm (simple or grid) = 
ns_type                  = grid
; Periodic boundary conditions: xyz or no = 
pbc                      = xyz

; Neighbor list should be at least 2 A greater than the either rcut or rvdw

; nblist cut-off         = 
rlist                    = 1.15


; OPTIONS FOR ELECTROSTATICS AND VDW: These parameters were all optimized for fast and accurate small molecule calculations.
; See Shirts and Paliwal (2011)

; Method for doing electrostatics = 
coulombtype              = PME-Switch
rcoulomb-switch          = 0.88
rcoulomb                 = 0.9

; Method for doing Van der Waals = 
vdw-type                 = Switch
; cut-off lengths        = 
rvdw-switch              = 0.85
rvdw                     = 0.9
; Spacing for the PME/PPPM FFT grid = 
fourierspacing           = 0.12
; EWALD/PME/PPPM parameters = 
pme_order                = 4
ewald_rtol               = 1e-04
ewald_geometry           = 3d
epsilon_surface          = 0

; Apply long range dispersion corrections for Energy and Pressure = 
DispCorr                 = EnerPres

---------------
; Slow temperature and pressure coupling that won't disturb the dynamics too much.  Parrinello-Rahman 
; gives very close to accurate volume distributions (Shirts, JCTC 2012)
---------------

gen_vel                  = no


; constrain the hydrogen bonds, allowing longer timesteps.
; Better to choose a higher lincs order just to be sure that 
; the constraints are obeyed to high precision; it's not that expensive.
constraints              = hbonds
; Type of constraint algorithm = 
constraint-algorithm     = lincs
; Highest order in the expansion of the constraint coupling matrix = 
lincs-order              = 12

;--------------------
; Free energy parameters
free-energy               = yes

sc-alpha                  = 0.5 
sc-r-power                = 6 
sc-power                  = 1  
; The following parameters describe a particularly efficient path 
; for small molecule solvation.  But it's not THAT much better 
; than the above choice, and it sometimes dies when run 
; in single precision 
;--------
;sc-alpha                 = 0.001  
;sc-power                 = 1  
;sc-r-power               = 48
;-------

; Which intermediate state are we simulating?
-------
init-lambda-state        = X

; What are the values of lambda at the intermediate states?
;------- 
coul-lambdas             = 0.0 0.2 0.5 1.0 1.0 1.0 1.0 1.0 1.0
vdw-lambdas              = 0.0 0.0 0.0 0.0 0.2 0.4 0.6 0.8 1.0 

; This makes sure we print out the differences in Hamiltonians between all states, and not just the neighboring states
;--------
calc-lambda-neighbors = -1

; the frequency the free energy information is calculated.  This 
; frequency (every 0.2 ps) is pretty good for small molecule solvation.
;-------
nstdhdl                  = 100 

; not required, but useful if you are doing any temperature reweighting.  Without 
; temperature reweighting, you don't need the total energy -- differences are enough
dhdl-print-energy        = yes

; We are doing free energies with the ethanol molecule alone
couple-moltype           = NMA
; we are changing both the  vdw and the charge.  In the initial state, both are on
couple-lambda0           = vdw-q
; in the final state, both are off.
couple-lambda1           = none
; we are keeping the intramolecular interactions ON in all the interactions from state 0 to state 8
couple-intramol          = no