From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Thu Oct 13 2011 - 07:14:53 CDT
Hi Lyna,
The "wall" potentials are actually soft, so the colvar is not strictly
constrained to be inside the range. In particular, if the colvar is
subject to high forces, the bias is not always enough to overcome
them. This could be the case here. Since the full range of the
coordinate is [0, 1], a force constant of 100 is not huge. You could
try a higher value.
Cheers,
Jerome
2011/10/12 Yun Luo <luoyun724_at_gmail.com>:
>
> 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!
>
> Lyna
>
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:57:49 CST