AMBER Archive (2004)

Subject: Re: AMBER: GB and langevin dynamics

From: David A. Case (
Date: Mon Sep 13 2004 - 14:59:31 CDT

On Thu, Sep 09, 2004, Sergio E. Wong wrote:
> I'm concerned b/c I ran a GB + langevin dynamics simulation of a short
> peptide (ACE GLY SER SER SER NME) and the average temperature (over
> 500,000 steps = 0.5 ns) is about 10 degrees above the target temperature.

I haven't seen this in simulations we have done. You might check that
energy is conserved wtih temperature coupling turned off (ntt=0) for your
system. Also worth checking is the value of nscm you use (try a value of
1000 or 2000), to see if that makes a difference. You could also try
increasing gamma_ln, but this shouldn't make a difference, and doesn't in
my test cases.

In the end, we may have to get your input files to see what is really are correct to be concerned about this sort of result.

...good luck...dac

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