From: Haleh a (halehabdi_at_sabanciuniv.edu)
Date: Mon Nov 02 2015 - 05:55:59 CST
Dear NAMD users,
Recently, I have been trying to run ABF simulations with RMSD as the
collective variables. I am using the following *.in file:
#rmsd.in
Colvarstrajfrequency 1000
Colvarsrestartfrequency 1000
colvar {
name RMSD
width 0.05
lowerboundary 0.1
upperboundary 1.25
lowerwallconstant 100.0
upperwallconstant 100.0
outputAppliedForce on
rmsd {
atoms {
psfSegID P1
atomNameResidueRange CA 1-159
atomsFile main_abf.pdb
atomsCol B
atomsColValue 1.0
}
refPositionsFile ref_abf.pdb
refPositionsCol B
refPositionsColValue 1.0
}
}
abf {
colvars RMSD
fullSamples 1000
}
I am getting the following error on NAMD 2.10 on a cluster :
colvars:
----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2012-03-23.
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 1000
colvars: # colvarsRestartFrequency = 1000
colvars: # colvarsTrajAppend = off [default]
colvars: The restart output state file will be "abf.colvars.state".
colvars: The final output state file will be "abfo.colvars.state".
colvars: The trajectory file will be "abfo.colvars.traj".
colvars:
----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = RMSD
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.
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Error in the collective variables module: exiting.
I tried running the same script on NAMD 2.9 on my desktop. It does not give
me the same error. However, my Abf.colvar.state and abf.pmf files are empty
as follows:
abf.pmf file:
xi A(xi)
0.1 0
0.15 0
0.2 0
0.25 0
0.3 0
0.35 0
0.4 0
0.45 0
0.5 0
0.55 0
0.6 0
0.65 0
0.7 0
0.75 0
0.8 0
0.85 0
0.9 0
0.95 0
1 0
1.05 0
1.1 0
1.15 0
1.2 0
1.25 0
and
Abf.colvar.state
configuration {
step 1104000
dt 1.00000000000000e+000
}
colvar {
name RMSD
x 1.56341258634097e+000
}
abf {
configuration {
name abf1
}
samples
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0
gradient
0 0 0
0 0 0
0 0 0
0 0 0
0 0 0
0 0 0
0 0 0
0 0
}
Any suggestion to remove the error and help me get more clear on the
subject is highly appreciated.
Best regards,
Haleh
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