From: Basak Isin (isinbasak_at_yahoo.com)
Date: Fri Aug 02 2013 - 16:35:11 CDT
----- Original Message -----
From: "Beaven, Andrew" <a607b333_at_ku.edu>
To: "<namd-l_at_ks.uiuc.edu>" <namd-l_at_ks.uiuc.edu>
Cc:
Sent: Friday, August 2, 2013 2:29 PM
Subject: namd-l: Changing NAMD XY restraint
Hi - is there a way I can continually update the target position for a harmonic restraint? I'm trying to restrain two protein monomers at the maximal distance away from each other. I see that I could simply use the numerical value of the initial 0.25*$boxa (which is ~18 Å), but I'd like the target value to fluctuate with the box size during the simulation (since I'm starting from a non-equilibrated system). When I use the numerical value, the job runs and appears to keep the monomers in the desired locations, but as mentioned, this isn't exactly what I want…
In my NAMD input file (along with the other simulation variables), I use:
colvars on
colvarsConfig /path/restraint.col
The /path/restraint.col file is shown below.
Thank you,
Andrew
################################################
Colvarstrajfrequency 100
Colvarsrestartfrequency 100
colvar {
name proa_rest
distanceXY {
ref {
dummyAtom ( -0.25*$boxa, -0.25*$boxa, 0.000 )
}
main {
atomsFile /path/proa.ref
atomsCol B
atomsColValue 1.0
}
}
}
colvar {
name prob_rest
distanceXY {
ref {
dummyAtom ( 0.25*$boxa, 0.25*$boxa, 0.000 )
}
main {
atomsFile /path/prob.ref
atomsCol B
atomsColValue 1.0
}
}
}
harmonic {
colvars proa_rest
centers 0.0
forceConstant $fc
}
harmonic {
colvars prob_rest
centers 0.0
forceConstant $fc
}
################################################
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