From: Yun Luo (luoyun724_at_gmail.com)
Date: Wed Sep 28 2011 - 15:38:02 CDT
Dear NAMD developers,
I want to use ABF with colvar "alpha" for a ten-alanine peptide. It seems work when I tested my script on linux cluster. But when I use NAMD2.8 on Blue Gene/P supercomputer, the output gives error message as below:
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = alpha
colvars: Initializing a new "alpha" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # psfSegID = HLX
colvars: # hBondCoeff = 0.5
colvars: # hBondCutoff = 3.3
colvars: # hBondExpNumer = 6
colvars: # hBondExpDenom = 8
colvars: Error: cannot add atoms to a dummy group.
colvars: If this error message is unclear, try recompiling with -DCOLVARS_DEBUG.
FATAL ERROR: Error in the collective variables module: exiting.
-----------------------------------------------------------------------------------------
Is this a bug related to supercomputer version?
My colvar and abf input file is shown as below:
colvarsTrajFrequency 100
colvarsRestartFrequency 100
colvar {
name alpha
width 0.1
lowerboundary 0.0
upperboundary 1.0
lowerwallconstant 10.0
upperwallconstant 10.0
extendedLagrangian on
alpha {
residuerange 1-10
psfSegID HLX
hbondcoeff 0.5
angleref 88
angletol 15
hbondcutoff 3.3
hbondexpnumer 6
hbondexpdenom 8
}
}
abf {
colvars alpha
fullSamples 10000
applyBias yes
outputFreq 100
hideJacobian no
}
Thanks !
Lyna
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