Boundary potential of colvar alpha not working?

From: Yun Luo (
Date: Wed Oct 12 2011 - 09:34:27 CDT

Dear NAMD supporter,

I'm using "alpha" colvar for a deca-alanine peptide in vacuum. I set up the boundary for alpha 0.0 to 2.5 as below. And I increased the wallconstant and decrease the extendedFluctuation as below. However, during 2 ns the configuration just stays stable at the region outside of by alpha boundary. It seems to me that no matter what constant I use, the boundary potential is not working for alpha colvar, no matter extendedLagrangian is turned on or off. I tested with distance colvar, the boundary potential works well though.
The outputAppliedForce is fluctuating between -2000 and 2000, but average around 0.
The outputSystemForce is 0.
The MISC in NAMD's energy output is fluctuating between 0 and 5, but average around 1.
The Boundary in NAMD's energy output is 0.


colvarsTrajFrequency 100
colvarsRestartFrequency 100000

colvar {
  name alpha
  width 0.01
  lowerboundary 0.0
  upperboundary 0.25
  lowerwallconstant 100.0
  upperwallconstant 100.0
  extendedLagrangian on
  extendedFluctuation 0.0005
  outputValue on
  outputVelocity on
  outputEnergy on
  outputSystemForce on
  outputAppliedForce on

  alpha {
       residuerange 1-10
       psfSegID HLX
       hbondcoeff 0.5
       angleref 88
       angletol 15
       hbondcutoff 3.3
       hbondexpnumer 6
       hbondexpdenom 8


Thanks a lot!


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