From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Aug 26 2013 - 08:49:08 CDT
Indeed, by reducing langevinDamping you are basically reducing the
viscosity of the system as well as the coupling to the random forces,
basically making any existing instabilities in the simulation more
apparent. You can try equilibrating you system using higher damping and
then slowly reduce the coupling to the desired value. Not that at 0.1
inverse picoseconds your temperature may fluctuate more than you may like
(so check for that).
On 26 August 2013 15:24, Jose Borreguero <borreguero_at_gmail.com> wrote:
> Dear NAMD gurus,
> I am several NPT equilibrium simulations with langevinPistonPeriod=100 and
> langevinDamping=0.1 (manual recommends langevinDamping=5) because I wanted
> a light coupling of the system with the thermal bath.
> A few of the simulations aborted with the following message:
> "ERROR: Atoms moving too fast; simulation has become unstable."
> Could a small damping coefficient lead to such errors? If so, what would
> be the scenario giving rise to some atom moving too fast?
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:34 CST