From: Naiyin Yu (nyyu_at_brandeis.edu)
Date: Sun Jan 17 2010 - 00:32:57 CST
Dear All,
I am trying to use "colvar" to constrain the distance between two
monomers when I equilibrate the system before the simulation. The
problem is after heating to the certain temperature (step by step),
the system started to equilibrate with harmonic constraint on the two
monomers. While it failed at the first step and the namd output
showed like:
ERROR: Atom 35 velocity is nan nan nan (limit is 6000)
..
..
and the error file gave the following message:
------------ Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Periodic cell has become too small for original
patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
I have already enlarge the margin or change the forceConstant but
nothing new happened. Does anyone know what's the problem?
Here is the script I use:
colvar {
name com
width 2.5
outputSystemForce off
outputAppliedForce on
distance {
group1 {
atomsFile Acom.pdb
atomsCol O
atomsColValue 2.0
}
group2 {
atomsFile Bcom.pdb
atomsCol O
atomsColValue 2.0
}
}
}
harmonic {
colvars com
forceConstant 0.1
centers 24
}
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