Re: ABF simulation with extendedLagrangian on keeps crashing

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Wed Apr 20 2011 - 09:22:21 CDT

Hi,

Just for fun, I run from the last restart file, writing each step to the
DCD. The last agonizing moments (in graphical form) can be found
here<http://www.ijs.si/ijs/dept/epr/ajasja/mails/ABF/crash.gif>.
The two atoms included in the ABF are the CB atom and the last oxygen of the
side-chain. The potential and kinetic energies of the fictive particles
are getting larger, but stay finite. If to much energy is transited into the
spring, then I should try with a heavier particle and a weaker
spring constant, right?

theta
step potential kinetic
11000 2.15652342996330e-002 3.18990492159784e-004
792187 1.10846675128305e+002 2.83213123555579e+001

phi
step potential kinetic
11000 1.31686077436764e-001 1.69791759804012e-002
792187 1.78364015718248e+002 2.96619241022563e+002

The simulation normally crashes somewhere between 2 ns and 15 ns (I have
done many runs allready:)
Perhaps the fixed dummy atoms in the definition of the colvars could be
problematic as well?

Best regards,
Ajasja

colvar {
  name theta

  width 5
  lowerboundary 0
  upperboundary 180
  lowerWallConstant 10
  upperWallConstant 10

  extendedLagrangian on

  angle {

    group1 { dummyAtom (3.283, -0.213, 99.366) } ; #100 A above CB
    group2 { atomnumbers 204 } ;#CB
    group3 { atomnumbers 173 } ;#O1
  }
}

colvar {
  name phi

  width 5
  lowerboundary -100
  upperboundary +100
  lowerWallConstant 10
  upperWallConstant 10

  extendedLagrangian on

  dihedral {
    group1 { atomnumbers 173 } ;#O1
    group2 { atomnumbers 204 } ;#CB
    group3 { dummyAtom (3.283, -0.213, -100.63) } ; #100 A below CB
    group4 { dummyAtom (13.283, -0.213, -100.63) } ; #100 A below and 10 in
the x direction from CB
  }
}

> I still found no reason why the ABF simulation is crashing though.
>
> Best regards,
> Ajasja
>
> 2011/4/19 Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>
>
>> Hi,
>>
>> I'm not getting any output of the PMF in the metadynamics simulations, for
>> which I have also kept extendedLagrangian on.
>> These simulations run OK, but don't give me a PMF output. (I should
>> have probably mentioned this in a separate e-mail as it is unrelated to the
>> ABF crashing).
>>
>> For the ABF simulations: I looked through the colvar traj file, but I
>> don't notice anything unusual. The energies are low and the r_XXX are
>> similar to the colvar values. I'm attaching the traj file.
>>
>> Thank you & best regards,
>> Ajasja
>>
>>
>>
>> On Tue, Apr 19, 2011 at 18:41, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>wrote:
>>
>>> Hi Asjasja, did you check the trajectory of the moving restraint centers
>>> aka fictitious masses? Because you have few degrees of freedom in an in
>>> vacuo system, the chance of transmitting energy to the harmonic spring may
>>> be high.
>>>
>>> So you may have too much energy transmitted to the harmonic spring, and
>>> the centers may have gone far from the actual values of the colvars. This
>>> could explain why you got no PMF output (the colvars are way off the grid)
>>> and in some cases instability (harmonic forces too strong).
>>>
>>> Giacomo
>>>
>>> ---- ----
>>> Giacomo Fiorin - Postdoctoral Researcher
>>> ICMS - Institute for Computational Molecular Science - Temple
>>> University
>>> 1900 N 12 th Street, Philadelphia, PA 19122
>>> giacomo.fiorin_at_temple.edu
>>> ---- ----
>>>
>>>
>>>
>>>
>>> On Tue, Apr 19, 2011 at 12:05 PM, Ajasja Ljubetič <
>>> ajasja.ljubetic_at_gmail.com> wrote:
>>>
>>>> This is strange: I sent the whole mail, but it seems only half got sent
>>>> though the list. Trying again...
>>>> Dear all,
>>>>
>>>> I have a 2D ABF simulation that keeps crashing after several ns.
>>>> The error is:
>>>> ERROR: Constraint failure in RATTLE algorithm for atom 202!
>>>> ERROR: Constraint failure; simulation has become unstable.
>>>> ERROR: Exiting prematurely; see error messages above.
>>>> (this atom is the hydrogen connected to the beta carbon)
>>>>
>>>> if I turn rigid bonds of I get:
>>>> FATAL ERROR: High global exclusion count! System unstable or
>>>> pairlistdist
>>>> or cutoff too close to periodic cell size.
>>>>
>>>> FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
>>>>
>>>> The metadynamics simulation with the same colvars appears to be ruining
>>>> OK
>>>> (but it's not writing a PMF)
>>>>
>>>> The system is an alanine alpha helix in vacuum, spin-labelled at the
>>>> middle
>>>>
>>>
>>>
>>
>

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