From: Vince Cho (vince_at_fastmail.fm)
Date: Wed Dec 25 2013 - 05:31:26 CST
Hello All,
I am trying to calculate the PMF of my system via ABF method, using
dihedral angle as my reaction coordinate with colvars command. However,
I would also like to restrain some distances during this simulation.
>From the ABF documentation
(http://www.ks.uiuc.edu/Research/namd/2.6/ug/node35.html), I have found
that restraintList option was available, but when I tried it an error
occurred saying that this keyword cannot be recognised.
I have a feeling that when I load abf within colvars command, there is
only a limited number of commands that I can use within that, but I'm
not sure. Anyway, could you please take a look at my conf and in files
and see where it went wrong?
Here is how I call Colvars.in from my .conf file:
colvars on
colvarsConfig Colvars.in
And the Colvars.in file looks like:
colvarsTrajFrequency 500
colvarsRestartFrequency 5000
colvar {
name phi
width 0.5
lowerboundary 3
upperboundary 9
lowerWallConstant 0.2
upperWallConstant 0.2
dihedral {
group1 {
atomsFile l1_atom.pdb
atomsCol O
atomsColValue 1.0
}
group2 {
atomsFile l1_atom.pdb
atomsCol O
atomsColValue 2.0
}
group3 {
atomsFile l1_atom.pdb
atomsCol O
atomsColValue 3.0
}
group4 {
atomsFile l1_atom.pdb
atomsCol O
atomsColValue 4.0
}
}
}
abf {
colvars phi
fullSamples 500
abf restraintList {
dist1 {dist {P1 2 CA} {P5 2 CA} 40.0 16.0}
dist2 {dist {P1 13 CA} {P5 13 CA} 40.0 16.0}
dist3 {dist {P2 2 CA} {P6 2 CA} 40.0 16.0}
dist4 {dist {P2 13 CA} {P6 13 CA} 40.0 16.0}
dist5 {dist {P3 2 CA} {P7 2 CA} 40.0 16.0}
dist6 {dist {P3 13 CA} {P7 13 CA} 40.0 16.0}
dist7 {dist {P4 2 CA} {P8 2 CA} 40.0 16.0}
dist8 {dist {P4 13 CA} {P8 13 CA} 40.0 16.0}
}
}
And like I said above, the "restraintList" keyword doesn't seem to be
recognised.
Thanks in advance, and Merry Christmas to all!
-- Wovon man nicht sprechen kann, daruber muss man schweigen.
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