Re: Boundary potential of colvar alpha not working?

From: Yun Luo (luoyun724_at_gmail.com)
Date: Thu Oct 13 2011 - 08:21:15 CDT

Thanks Jerome! I think I tried the wall potential constant until 1000. But I can try with even higher constant (Is it a quadratic harmonic potential?) But what about the extendedLagrangian force constant? Does it necessary ? If yes, how to balance to wall force constant with extendedlagrangian force constant?

Thanks!

Lyna

On Oct 13, 2011, at 7:14 AM, Jérôme Hénin wrote:

> 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
>>
>>

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