Make a molecule dissapear in gromacs

This is a free energy perturbation basics – making molecules appear and disappear and using that to estimate free energies.

This code can also be used ror other, imaginative purposes. To make a molecule 'Ligand' disappear, use the following

grompp.mdp
...
integrator = ld
dt = 0.001
nsteps = 10000
...
; FREE ENERGY
free_energy          = yes
init_lambda          = 0.00
delta_lambda         = 1e-4
sc-alpha             = 1.5 #
sc-power             = 1.0
couple-moltype       = Pore
couple-lambda0       = vdw-q
couple-lambda1       = none

Now let's break it down:
free_energy = yes  is an on-switch for this feature of gromacs
init_lambda = 0.0 defines how invisible is the molecule at the start of the run, a value of 0 indicates that it's fully visible

delta_lambda = 1e-4 will define by how much the molecule is disappeared at every step of the simulation. Here this has to match the nsteps value - after 10000 steps the molecule will be fully gone.

couple-lambda0 = vdw-q shows that at the start of the simulation both the van der Waals  (vdw) and charged (q) interactions are turned on

 couple-lambda1 = none will make that both the vdw and q are turned off at the end of the run.

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