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G_hyd using FEP with Gromacs
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; RUN CONTROL PARAMETERS = | |
integrator = sd | |
; start time and timestep in ps = | |
tinit = 0 | |
dt = 0.002 | |
; 6 ns. This turns out to be long enough for systems without slow intramolecular degrees of freedom | |
nsteps = 1000000 | |
; 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 = | |
nstcomm = 10 | |
; Output frequency for energies to log file and energy file = | |
nstlog = 1000 | |
nstenergy = 100 | |
; NEIGHBORSEARCHING PARAMETERS = | |
; nblist update frequency = | |
nstlist = 10 | |
; 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) | |
--------------- | |
; Groups to couple separately = | |
tc-grps = System | |
; Time constant (ps) and reference temperature (K) = | |
tau_t = 5.0 | |
ref_t = 300 | |
; Pressure coupling = | |
Pcoupl = Parrinello-Rahman | |
; Time constant (ps), compressibility (1/bar) and reference P (bar) = | |
tau_p = 5.0 | |
compressibility = 4.5e-5 | |
ref_p = 1.01325 | |
; We don't strictly need these, because it already has velocities | |
; that are at the right temperature. But including this is safer. | |
---------- | |
gen_vel = no | |
continuation = yes | |
; 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 |
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