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Article ID: 1574 - Last Modified: August 23, 2011

I would like to customize the lambda schedule for FEP jobs. How can I do that?

For relative FEP jobs, you can modify the task stage in your .msj file to look like like the following:

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]
}
# other stuff
}
}
task = "desmond:fep"
}

where the fep.lambda map is the custom schedule. Since it's inside the set_family map, it will be 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 do a similar modification to the .msj file:

task {
set_family = {
desmond = {
fep.lambda = {
vdw = [0.0 0.17455359999999998 0.28162879999999996 0.50142720000000018 1.0 1.0 1.0
1.0]
coulomb = [0.0 0.0 0.0 0.0 0.0 0.33333333333333337 0.66666666666666674 1.0]
}
# other stuff
}
}
task = "desmond:fep"
}

If you only want to customize the number of windows (i.e. still use the default scheme), you can do something like the following (for both relative or absolute FEP jobs):

task {
set_family = {
desmond = {
fep.lambda = "default:8" # 8 windows
# other stuff
}
}
task = "desmond:fep"
}

Keywords: Desmond

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