From: David Minh (daveminh_at_gmail.com)
Date: Fri Oct 26 2012 - 11:13:21 CDT
Hello NAMD users and developers,
I am having a strange issue related to colvars. I am trying to do a
coorfile loop in my NAMD configuration file:
coorfile open dcd {begin1.dcd}
while { ![coorfile read] } {
reinitvels $temperature
run 100
}
coorfile close
It works fine if I remove the lines:
colvars on
colvarsConfig gorgeCylinder.colvars
Here are contents of gorgeCylinder.colvars:
colvar {
name DistXY
upperWall 6.0
upperWallConstant 10.0
distanceXY {
main {
atomsFile {../../../ligands/AAA/ligand.grid.pdb}
atomsCol B
atomsColValue 1.0
}
ref {
dummyAtom (52.548195, 57.459400, 49.528568)
}
axis (-0.294390, -0.561701, 0.773192)
}
}
colvar {
name DistZ
lowerWall 3
upperWall 25
lowerWallConstant 10.0
upperWallConstant 10.0
distanceZ {
main {
atomsFile {../../../ligands/AAA/ligand.grid.pdb}
atomsCol B
atomsColValue 1.0
}
ref {
dummyAtom (52.548195, 57.459400, 49.528568)
}
axis (-0.294390, -0.561701, 0.773192)
}
}
Basically it keeps the molecule within a cylinder.
If I include the colvars lines in the NAMD configuration file, the code
runs for 100 steps and then says:
FATAL ERROR: Got the wrong number of atoms
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Got the wrong number of atoms
Charm++ fatal error:
FATAL ERROR: Got the wrong number of atoms
Any ideas on what could cause this? The error doesn't really make sense
because it works fine without the colvars lines. Is the error really
related to colvarsInput? I can't seem to put a colvarsInput into the tcl
loop.
Thanks,
David Minh
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