AMBER Archive (2006)

Subject: AMBER: Langevin temperature control vs berendson heat bath

From: Hayden Eastwood (s0237717_at_sms.ed.ac.uk)
Date: Wed Nov 29 2006 - 12:12:16 CST

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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