From: Vidhya Sankar (vidhyasankar7928_at_yahoo.com)
Date: Thu Jul 29 2021 - 07:50:15 CDT
Dear Namd users i tried form metadybamics us RMSD as CV i have following input files
colvar {
name s
width 1
lowerboundary 70
upperboundary 145
lowerwallconstant 10.0
upperwallconstant 10.0
scriptedFunction source.tcl
# extendedLagrangian on
# extendedFluctuation 0.01
rmsd {
group1
atomNumbersRange 1-1589
refpositionsfile 0.pdb
componentExp 1 }
rmmsd {
group2
atomNumbersRange 1-1589
refpositionsfile 1000.pdb
componentExp 2 }
rmsd {
group3
atomNumbersRange 1-1589
refpositionsfile 2000.pdb
componentExp 3 }
rmsd {
group4
atomNumbersRange 1-1589
refpositionsfile 3000.pdb
componentExp 4 }
group5
atomNumbersRange 1-1589
refpositionsfile 4000.pdb
componentExp 5 }
rmsd {
group6
atomNumbersRange 1-1589
refpositionsfile 5000.pdb
componentExp 6 }
rmsd {
group7
atomNumbersRange 1-1589
refpositionsfile 6000.pdb
componentExp 7 }
rmsd {
group8
atomNumbersRange 1-1589
refpositionsfile 7000.pdb
componentExp 8 }
rmsd {
group9
atomNumbersRange 1-1589
refpositionsfile 8000.pdb
componentExp 9 }
rmsd {
group10
atomNumbersRange 1-1589
refpositionsfile 9000.pdb
componentExp 10 }
}
#############################################################
# ABF section
#############################################################
abf {
colvars s
fullSamples 500
}
But when i run the meta dynamics i gt the following error
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration:
colvars: # smp = on [default]
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 1000
colvars: # colvarsRestartFrequency = 10000 [default]
colvars: # scriptedColvarForces = off [default]
colvars: # scriptingAfterBiases = off [default]
colvars: Warning: no collective variables defined.
colvars: Collective variables initialized, 0 in total.
colvars: No collective variables biases were defined.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module (re)initialized.
colvars: ----------------------------------------------------------------------
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "pathCV1.in":
colvars: Error: unmatched curly braces in configuration.
FATAL ERROR: Error in the collective variables module: exiting.
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Error in the collective variables module: exiting.
What are the mistake i did it would be useful if any one of you pointed out Even i tried lot i could not trace out error
With regards
S.VIDHYASNKAR
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