Re: AMBER: Amber Poisson-Boltzmann MD :Equilibration Problem

From: David A. Case <>
Date: Tue, 1 Mar 2005 08:41:08 -0800

On Mon, Feb 28, 2005, praveena moldy wrote:
> I want to run Poisson-Botzmann MD in NVE ensemble for a small peptide
> Ace-Ala3-NMe with the length of all bonds fixed. I have to
> equilibrate it to 300K slowly within 100ps.The time step of the
> simulaiton which I kept is 1fs. In the first 65ps the molecule is
> made to heat gradually to 300K, and in the successive 25ps the
> temperature is restrained to 300K and no temperature scaling is
> adopted in the successive 10ps.
> The input I have used is the one below,
> ntt=0,ntc=3,ntf=3,

You are setting ntt=0, so that there is no temperature regulation; the
value to temp0 is ignored in this case. Check the temperature profile
of your run. For early simulations, set ntpr to a small value (like 1)
and just run 1000 steps or so, to make sure that things are working the way
you want them to. Then you can attempt longer runs.


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Received on Tue Mar 01 2005 - 16:53:00 PST
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