Umbrella Sampling in NAMD

From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Thu Nov 13 2014 - 10:25:13 CST

Dear NAMD users,

I am trying to do Umbrella Sampling to calculate the energy profile of a
protein penetrating a membrane. I have read over the manual but I am still
not clear about my colvar file. Would you please help me on this? I am
pasting below my distance.in.

Also
1)

What value should I choose for the forceConstant or to what exactly does it
depend on?
2) Am I choosing the right centers for my colvar? As the initial separation
between the protein and the membrane is 5A
and I am targeting at touching the membrane (so
​ ​
targetCenters
​ ​
0)
​.​

3) Am I choosing the right
targetNumSteps
as I want to run 1ns (with 1fs timestep) for each window of the US

Many thanks,
Kevin

distance.in:

Colvarstrajfrequency 1000
colvar {
name ProjectionZ
distanceZ {
main {
atomnumbers { "some selection of the protein" }
}
ref {
atomnumbers { "some selection of the membrane" }
}
axis (0.0, 0.0, 1.0)
}
}

harmonic {
colvars ProjectionZ
centers 5.0
forceConstant 10.0
targetCenters 0.0
targetNumSteps 1000000000
targetNumStages 30
}

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