Re: ABF simulation with extendedLagrangian on keeps crashing

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue Apr 19 2011 - 12:05:23 CDT

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 Ljubeti <
> 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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