From: Buddhadev Maiti (chebm_at_langate.gsu.edu)
Date: Wed Feb 16 2011 - 21:04:11 CST
Dear NAMD Users,
I am performing ABF calculation using RMSD as a collective variable. I am using NAMD-2.7 version. My Distance.in file is in below. I have simulated the system for 600ps. Now prod1.colvar.traj file is fine. The RMSD changed within the range of lower boundary and upper boundary. But I am getting PMF which is unreasonable. Could anybody please suggest me about this problem, it will be great help for me. The prod1.pmf file is below.
Have a nice day,
Thanks,
Maiti
Distance.in:
Colvarstrajfrequency 1000
Colvarsrestartfrequency 1000
colvar {
name GRrmsd
width 0.1
lowerboundary 0.856
upperboundary 2.856
lowerwallconstant 100.0
upperwallconstant 100.0
rmsd {
atoms {
atomsFile 1.pdb
atomsCol O
atomsColValue 1.0
}
refPositionsFile ep.pdb
refPositionsCol O
refPositionsColValue 1.0
}
}
abf {
colvars GRrmsd
fullSamples 1000
}
prod1.pmf:
# xi A(xi)
0.856 1872.6269171991
0.956 1672.3918560045
1.056 1476.7095174407
1.156 1299.8228904008
1.256 1147.2512863577
1.356 1002.7524346827
1.456 871.97576066592
1.556 750.28495775502
1.656 629.72534760479
1.756 499.81354711714
1.856 366.1914525118
1.956 242.48506563451
2.056 131.70460778341
2.156 0
2.256 0
2.356 0
2.456 0
2.556 0
2.656 0
2.756 0
2.856 0
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