From: Subbarao Kanchi (ksubbu85_at_gmail.com)
Date: Sat Mar 08 2014 - 05:00:28 CST
Dear all,
I am using the fallowing colvar (distancez) to do umbrella
sampling.I used ref { atomNumbersRange 1-30208} to define reference
group,It makes simulation very slow (~1ns/4days) but If I use ref {
dummyAtom (0.0, 0.0, 0.0)} simulation is as fast as normal MD (~4ns/day).
If I used the dummy atom, the actual distance between center of masses
between two groups are not maintaining. I checked mailing list but I did
not find any discussion on this problem. I will appreciate any suggestions
in this regard.
Regards,
Subbarao Kanchi.
colvarsTrajFrequency 1000
colvarsRestartFrequency 1000
colvar {
width 0.5
name lipid
distancez {
main { atomNumbersRange 30209-31494}
ref { atomNumbersRange 1-30208}
axis (0.0, 0.0, 1.0)
}
}
harmonic {
colvars lipid
centers 57.97
forceConstant 500.0
targetCenters 60.0
targetNumSteps 1000000
}
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