From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Apr 19 2011 - 11:41:55 CDT
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
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:57:01 CST