[gmx-users] Hamiltonian replica exchange

[Qinghua Liao]

Hello Hind,

There HREMD is available for Gromacs patched with PLUMED, and there is a 
tutorial you can go through:
https://www.plumed.org/doc-v2.5/user-doc/html/hrex.html


All the best,
Qinghua

On 1/18/20 8:12 PM, hind ahmed wrote:
> 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
>