[gmx-users] Hamiltonian replica exchange

[hind ahmed]

Dear,
is there a tutorial to run Hamiltonian replica exchange in gromacs?? and could you please see if the mdp setting is right to run Hamiltonian replica exchange of lipid system using a coarse-grained method?

 integrator               = sd
tinit                    = 0.0
dt                       = 0.030
nsteps                   = 15000000

nstxout                  = 5000
nstvout                  = 5000
nstfout                  = 5000
nstlog                   = 5000
nstenergy                = 5000
nstxout-compressed       = 5000
compressed-x-precision   = 100

cutoff-scheme            = Verlet
nstlist                  = 20

ns_type                  = grid
pbc                      = xyz
verlet-buffer-tolerance  = 0.005

epsilon_r                = 15
coulombtype              = reaction-field
rcoulomb                 = 1.1
vdw_type                 = cutoff
vdw-modifier             = Potential-shift-verlet
rvdw                     = 1.1

tc-grps                  = membrane solute
tau_t                    = 1.0  1.0
ref_t                    = 323 323

; Pressure coupling:
Pcoupl                   = Parrinello-rahman
Pcoupltype               = isotropic
tau_p                    = 12.0
compressibility          = 4.5e-5
ref_p                    = 1.0

; Free energy control stuff
free_energy              = no
init_lambda_state        = 0
delta_lambda             = 0
calc_lambda_neighbors    = 1        ; only immediate neighboring windows
; Vectors of lambda specified here
; Each combination is an index that is retrieved from init_lambda_state for each simulation
; init_lambda_state        0    1    2    3    4    5    6    7    8    9    10   11
coul-lambdas             = 1.00 0.95 0.90 0.85 0.80 0.75 0.70 0.65 0.60 0.55 0.50 0.45
vdw-lambdas              = 1.00 0.95 0.90 0.85 0.80 0.75 0.70 0.65 0.60 0.55 0.50 0.45
bonded-lambdas           = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
restraint-lambdas        = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00

; Not doing simulated temperting here
temperature_lambdas      = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
; Options for the decoupling
sc-alpha                 = 0.5
sc-coul                  = yes       ; linear interpolation of Coulomb (none in this case)
sc-power                 = 1
sc-sigma                 = 0.3
couple-moltype           = CHOL ; name of moleculetype to decouple
couple-lambda0           = vdw-q      ; only van der Waals interactions
couple-lambda1           = none     ; turn off everything, in this case only vdW
couple-intramol          = no
nstdhdl                  = 10
; Do not generate velocities
gen_vel                  = no
; options for bonds
constraints              = none
; Type of constraint algorithm
constraint-algorithm     = lincs
; Constrain the starting configuration
; since we are continuing from NPT
continuation             = yes
; Highest order in the expansion of the constraint coupling matrix
refcoord_scaling         = all

Regards,
Thanks