ABF calculation using RMSD

From: Buddhadev Maiti (chebm_at_langate.gsu.edu)
Date: Mon Feb 14 2011 - 19:08:32 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. But in prod1.colvars.traj file I am getting RMSD values which are not in between 0.742 and 2.742. The prod1.colvars.traj is big file, so I am sending some of the values. Could anybody can suggest me any problem in Distance.in file, it will be great help for me.
Have a nice day,
Thanks,
Maiti

Distance.in
Colvarstrajfrequency 1000
Colvarsrestartfrequency 1000
colvar {
name GRrmsd
width 0.1
lowerboundary 0.742
upperboundary 2.742
lowerwallconstant 100.0
upperwallconstant 100.0
rmsd {
atoms {
atomsFile 10.pdb
atomsCol O
atomsColValue 1.0
}
refPositionsFile ep.pdb
refPositionsCol O
refPositionsColValue 1.0
}
}
abf {
colvars GRrmsd
fullSamples 1000
hideJacobian
}

prod1.colvars.traj:
       20000 8.80246428132221e-02
       21000 8.80608759027566e-02
       22000 8.46306414199712e-02
       23000 9.66174831058771e-02
       24000 9.94028080033878e-02
       25000 8.68121250316395e-02
       26000 8.61812497752078e-02
       27000 9.75722872880951e-02
       28000 9.28331687685522e-02
       29000 8.47315102606470e-02
       30000 9.97560581467597e-02
       31000 1.00552660409621e-01
       32000 8.92195009776420e-02
       33000 8.92411507759293e-02

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