From: Yun Luo (luoyun724_at_gmail.com)
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.
Thanks a lot!
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