Re: Boundary potential of colvar alpha not working?

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Thu Oct 13 2011 - 08:54:35 CDT

Hi Lyna,

I can't say anything more specific unless you tell me roughly what you
are trying to achieve.

Jerome

On 13 October 2011 15:21, Yun Luo <luoyun724_at_gmail.com> wrote:
> 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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