From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue Apr 19 2011 - 12:43:12 CDT
This is slightly embarrassing, but during testing I had the restart
frequency the set to the length of the simulation. I thought the
*dumpFreeEnergyFile
*dumps every colvarsTrajFrequency, but it dumps every
colvarsRestartFrequency.
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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