From: Victor Kwan (vkwan8_at_uwo.ca)
Date: Sun Dec 03 2017 - 05:12:06 CST
Hi all,
I am trying to set rmsd constrain for one of my runs and for some reason
the colvars molecule can't find the definition for atom group "atoms". I
have manually set the B column of the atoms to be constrained to 1.0
manually.
Any ideas?
rmsd.conf:
colvarsTrajFrequency 2000
colvarsRestartFrequency 20000
colvar {
name r1
width 0.1 #
#lowerboundary
#upperboundary
#lowerwallconstant
#upperwallconstant
rmsd{
atoms{
atomsFile merged.pdb
atomsCol B
atomsColValue 1.0
}
refPositionsFile merged.pdb # same as input
refPositionsCol B # XYZOB
refPositionsColValue 1.0
}
}
output:
colvars:
----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2015-09-16.
colvars: Using NAMD interface, version 2015-07-24.
colvars:
----------------------------------------------------------------------
colvars: Reading new configuration from file "rmsd.conf":
colvars: # indexFile = "" [default]
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 2000
colvars: # colvarsRestartFrequency = 20000
colvars: # colvarsTrajAppend = off [default]
colvars:
----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = r1
colvars: Initializing a new "rmsd" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: Error: definition for atom group "atoms" not found.
colvars: If this error message is unclear, try recompiling with
-DCOLVARS_DEBUG.
FATAL ERROR: Error in the collective variables module: exiting.
Thanks in advance,
VK
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