From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Mar 12 2011 - 11:16:19 CST
Hello:
As a beginner with colvars, probably I am posting pedestrian errors,
however I was unable to come out. I am trying (namd 2.8 Linux64) to
heat a protein in a membrane with harmonic restraints on chloride
anions pertaining to the protein. The .log relative to colvars reads:
Info: CREATING 13890 COMPUTE OBJECTS
Info: useSync: 1 useProxySync: 0
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2011-01-03.
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 100
colvars: # colvarsRestartFrequency = 200
colvars: # colvarsTrajAppend = off [default]
colvars: The restart output state file will be "./heat.restart.colvars.state".
colvars: The final output state file will be "./heat.colvars.state".
colvars: The trajectory file will be "./heat.colvars.traj".
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = colvar1
colvars: Initializing a new "distance" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # oneSiteSystemForce = off [default]
colvars: Initializing atom group "group1".
colvars: Atom group "group1" defined, 1 initialized: total mass = 35.45.
colvars: Initializing atom group "group2".
colvars: Atom group "group2" defined, 2 initialized: total mass = 28.014.
colvars: All components initialized.
colvars: # width = 1
colvars: # lowerBoundary = 0 [default]
colvars: # lowerWallConstant = 100
colvars: # lowerWall = -5
colvars: # upperBoundary = 10
colvars: # upperWallConstant = 100
colvars: # upperWall = 5
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = on
colvars: # outputAppliedForce = off [default]
colvars: Error: keyword "lower" is not supported, or not recognized
in this context.
colvars: If this error message is unclear, try recompiling with
-DCOLVARS_DEBUG.
FATAL ERROR: Error in the collective variables module: exiting.
____________________________
Below, an excerpt from the colvars .in file (inserted into the namd
the .conf file) showing the first colvar block and the harmonic block.
The other eight colvar
blocks have identical layout:
colvarsTrajFrequency 100 # output values every 100 steps (default)
colvarsRestartFrequency 200 # must be > colvarsTrajFrequency
colvar {
name colvar1 # needed to identify the variable
width 1.0 # twice the standard deviation during
# very short simulation; default 1.0
lower boundary -10.0
upperboundary 10.0
lowerWall -5.0 # a lttle higher than lowerBoundary
upperWall 5.0 # a little lower than upperBoundary
lowerWallConstant 100.0 # force constant in kcal/mol
upperWallconstant 100.0
outputSystemForce yes # reports also the system force on this
# colvar in addition to the current value
distance {
group1 {
atomNumbers 6763 # CLA427A(O1)
}
group2 {
atomNumbers 4327 4324 # NH1 NE of ARG273A(P1)
}
}
}
.......................................
harmonic {
name CLA_harmonic
colvars colvar1 colvar2 colvar3 colvar4 colvar5
colvar6 colvar7 colvar8 colvar9
centers 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
forceConstant 100.0
}
Thanks for help
francesco pietra
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