From: Peterson J (peterson.jjjj_at_gmail.com)
Date: Mon Sep 16 2013 - 23:02:55 CDT
Hello NAMD users,
I'm new to NAMD and trying to use colvar modules to do a biased simulation.
I am actually trying to use distancevec to move a part of my protein to a
desired position. After reading my colvarConfig file NAMD crashes with a
Segmentation Fault error message.
Can anyone help me with the possible reason to solve this? Below is the
error.
colvars:
----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2012-03-23.
colvars: # analysis = off
colvars: # colvarsTrajFrequency = 1
colvars: # colvarsRestartFrequency = 5000 [default]
colvars: # colvarsTrajAppend = off
colvars: The restart output state file will be
"colvar-tmd1.restart.colvars.state".
colvars: The final output state file will be "colvar-tmd1.colvars.state".
colvars: The trajectory file will be "colvar-tmd1.colvars.traj".
colvars:
----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = 1
colvars: Initializing a new "distancevec" 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, 7 initialized: total mass =
84.077.
colvars: Initializing atom group "group2".
colvars: Atom group "group2" defined, 7 initialized: total mass =
84.077.
colvars: All components initialized.
colvars: # width = 2
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = on
colvars: # outputSystemForce = off [default]
colvars: # outputAppliedForce = on
colvars:
----------------------------------------------------------------------
colvars: Collective variables initialized, 1 in total.
colvars:
----------------------------------------------------------------------
colvars: Initializing a new "harmonic" instance.
colvars: # name = harm
colvars: # colvars = { 1 }
colvars: # forceConstant = 20000
colvars: The force constant for colvar "1" will be rescaled to 5000
according to the specified width.
colvars: # centers = { ( 0 , 0 , 0 ) }
colvars: # targetCenters =
colvars: # targetForceConstant = 0 [default]
colvars: # targetNumSteps = 1000000
colvars: # targetNumStages = 0 [default]
colvars: # targetForceExponent = 1 [default]
colvars:
----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars:
----------------------------------------------------------------------
colvars: Collective variables module initialized.
colvars:
----------------------------------------------------------------------
Info: Startup phase 8 took 0.146609 s, 258.348 MB of memory in use
Info: Startup phase 9 took 0.000148058 s, 258.348 MB of memory in use
Info: Startup phase 10 took 0.00133204 s, 293.688 MB of memory in use
Info: Finished startup at 4.76158 s, 293.688 MB of memory in use
TCL: Running for 1000000 steps
Segmentation fault
Thanks,
Peterson
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