AMBER Archive (2006)

Subject: Re: AMBER: Langevin temperature control vs berendson heat bath

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Thu Nov 30 2006 - 06:06:22 CST

Hi,
> 1. Is there a minimum system size limit that you recommend for langevin
> dynamics? I.e. does langevin temperature control cease to work effectively
> when the system size is small?
...Langevin temperature control works with *any* system size,
even a single harmonic oscillator (where Berendsen-TC might give NaNs).

> 2. Is there a problem with my random number generator? If the collisions are
> indeed random then surely the net force over a long simulation period should
> approach 0? I.e. It seems suspicious that collisions don't balance out the
> translation of the molecule more.
...No need to worry. Random collisions *don't* cancel (at least not the
way you seem to expect them to), otherwise there would be no Brownian
motion.

good luck
Andreas
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu