Re: [AMBER] why total energy of the system is on the rise in NVE ensemble

From: David A Case <>
Date: Wed, 15 Oct 2014 08:58:12 -0400

On Tue, Oct 14, 2014, Hector A. Baldoni wrote:
> For solvated NVE simulations use something like this:

Your file looks OK to me: what is the slope of the energy vs time plot?
How many degrees of freedom do you have? A typical statistic is energy drift
(in units of kT) per degree of freedom per nanosecond, e.g:

%A R. Salomon-Ferrer
%A A.W. Goetz
%A D. Poole
%A S. Le Grand
%A R.C. Walker
%T Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2.
Explicit solvent particle mesh Ewald
%J J. Chem. Theory Comput.
%V 9
%P 3878-3888
%D 2013

You should compare you numbers to those in Table 7 of this paper.

...hope this helps...dac

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Received on Wed Oct 15 2014 - 06:00:04 PDT
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