AMBER Archive (2006)

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

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Wed Nov 29 2006 - 13:02:20 CST

which amber version, and have you applied all of the patches?
we have no such trouble with langevin dynamics and implicit solvent.

Hayden Eastwood wrote:

>Dear Amber guys
>
>I am doing simulations on a small (35 amino acids) peptide in an implicit
>solvent environment. I find that langevin temperature (using gamma_ln = 1)
>control results in a great deal of translational movement and rather little
>intra-molecular movement. Indeed, the dynamics of the regions that should be
>mobile appear to be quite "stiff". Dynamics with a Berendson thermostat
>appears to better reproduce the conformational behaviour of the 20 NMR
>structures.
>
>My questions are these:
>
>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?
>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.
>
>Many thanks
>
>hayden
>
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