From: Patrick Yee (pyee_at_nd.edu)
Date: Thu Apr 15 2010 - 22:19:45 CDT
Hi NAMD users,
I am having a problem with non-uniform sampling using ABF and colvars.
I did not have these sampling problems when using the TCL scripts for
ABF in NAMD 2.6. My sampling increases fairly linearly until the
simulation ends and even long simulations (10-20 ns) did not have
uniform sampling. Does anyone have any idea of why the sampling is not
uniform? I've given more details below.
I've just started using colvars (instead of the NAMD 2.6 TCL scripts)
for calculating a PMF with the ABF method. To test if the PMF would
work on my systems when I used the TCL script ABF method, I first
tried finding the PMF on pair of methane molecules in water and then
on Na+ and Cl- ions in water (the latter being from the tutorial); the
results matched very closely what I'd found from other MD simulations.
When I tried these same simulations in NAMD 2.7b2 with colvars, I
didn't get the correct PMF as I had using ABF with TCL scripts, most
likely because the sampling is not becoming uniform as the simulation
progresses. Note that with colvars I used fullSamples = 500, which was
the same as with the TCL script. I also thought the simulation might
not have been allowed to proceed long enough, but even after 10
million steps at 1fs/step, the sampling was very non-uniform. Sampling
ranges from 40000 when the groups are close and moves fairly linearly
to about 25000 as the groups move apart. I attached the colvars input
file I am using below. Again, please tell me why the sampling is not
becoming uniform.
Thank you in advance for your help.
Colvarstrajfrequency 2000
colvar {
name IonDistance
width 0.1
lowerboundary 0.05
upperboundary 13.00
lowerwallconstant 10
upperwallconstant 10
distance {
group1 {
atomnumbers { 1 }
}
group2 {
atomnumbers { 2 }
}
}
}
abf {
colvars IonDistance
fullSamples 500
}
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