RE: ABF calculation using RMSD

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Feb 16 2011 - 21:24:01 CST

Try running longer than 600 ps.

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Buddhadev Maiti
Sent: Wednesday, February 16, 2011 9:04 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: ABF calculation using RMSD

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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