How do I set up a custom lambda schedule for Desmond FEP jobs?

For relative FEP jobs, you can modify the task stage in the .msj file as follows:

task {
set_family = {
desmond = {
fep.lambda = { bondedA = [1.0 0.75 0.5 0.25 0.0] bondedB = [0.0 0.25 0.5 0.75 1.0]
chargeA = [1.0 0.75 0.5 0.25 0.0] chargeB = [0.0 0.25 0.5 0.75 1.0]
vdwA = [0.0 0.0 0.0 0.0 0.0] vdwB = [1.0 1.0 1.0 1.0 1.0] }
...
}
}
task = 'desmond:fep'
}

where the custom schedule is given in the fep.lambda map. Since the custom schedule is inside the set_family map, it is applied to all subsequent desmond family stages in the .msj file. Desmond family stages include: minimize, simulate, lambda_hopping, and replica_exchange.

For absolute FEP jobs, you can make a similar modification in the .msj file:

task {
set_family = {
desmond = {
fep.lambda = { vdw = [0.0 0.1745536 0.2816288 0.5014272 1.0 1.0 1.0 1.0] coulomb = [0.0 0.0 0.0 0.0 0.0 0.3333333333333333 0.6666666666666667 1.0]}
...
}
}
task = 'desmond:fep'
}

If you want to customize only the number of windows, and use the default scheme for the schedule, you can do the following:

task {
set_family = {
desmond = { fep.lambda = 'default:8' ... }
}
task = 'desmond:fep'
}

Here, 8 windows are specified with the default scheme.

Note that increasing the number of windows does not guarantee an improvement in the results, particularly if the lambda schedule is inappropriate for the system.

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