From: Vidhya Sankar (vidhyasankar7928_at_yahoo.com)
Date: Mon Aug 02 2021 - 03:31:16 CDT
Dear Namd users
I am using rmsd as CV in namd
for that i have input fie as follows
colvar {
name r1
width 1
lowerboundary 70
upperboundary 145
lowerwallconstant 10.0
upperwallconstant 10.0
# scriptedFunction source.tcl
# extendedLagrangian on
# extendedFluctuation 0.01
rmsd {
atoms { 1 2 3 4 5 }
atomsFile 0.pdb
atomsCol B
atomsColValue 1.0
# }
refpositionsfile 1000.pdb
refpositiosCol B
refPositionsColvValue 1.0
componentExp 1
}
}
But When i run the simulation I got error as follows
colvars: # scriptingAfterBiases = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = "r1"
colvars: Initializing a new "rmsd" component.
colvars: # name = "" [default]
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # scalable = on [default]
colvars: Initializing atom group "atoms".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: Error: no atoms defined for atom group "atoms".
FATAL ERROR: Error in the collective variables module: exiting.
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Error in the collective variables module: exiting.
It would be highly appreciable if any one point out and rectify the error for the past 10 days to me it was tedious to solve the error
With High regards
S.VIDHYA sankar
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