AMBER Archive (2008)

Subject: Re: AMBER: NVE energy and temperature drift

From: Lars Skjærven (lars.skjarven_at_biomed.uib.no)
Date: Fri Mar 07 2008 - 11:34:33 CST

Avg temperatures looks fine: 301.01, 301.00, 301.09, and 301.11 for the 1st,
2nd, 9th, and 10th nanosecond, respectively.

Regarding the size of the system, it is 220 amino acids, and ~32.000 atoms
with water molecules.

Thanks for your help. :-)

Lars

On Fri, Mar 7, 2008 at 5:32 PM, David A. Case <case_at_scripps.edu> wrote:

> On Fri, Mar 07, 2008, Lars Skjærven wrote:
> >
> > This is a follow up question to a thread in 2007 regarding NVE
> simulations (
> > http://structbio.vanderbilt.edu/archives/amber-archive/2007/3178.php). I
> had
> > the same problem with energy drifting. Thus, I followed the
> recommendations
> > from Case and Cheatham; lower shake tolerance, increase the accuracy of
> the
> > PME by reducing DSUM_TOL by an order of magnitude, and dt=0.001. The
> > simulation is much "smoother" now in terms of energy and temperature.
> The
> > shift has now been reduced to 5 kcal/mol (-75489 to -75484, first to
> last
> > step) during a 10ns simulation. The energy does not yet seem to
> converge.
> >
> > Should I be concerned about this energy drift, or is it small enough
> such
> > that I can accept it? My apologies if this has been answered earlier.
> >
>
> This depends somewhat on the size of your system, since the absolute drift
> will depend on how many atoms you have. In my experience, the total
> energy
> will never converge: it will just keep rising approximately linearly in
> time
> (at least up to 200 nsec, the longest single simulation I have).
>
> Here's the argument I often make: check the average temperature near the
> begining and the end (say over the first and last nanoseconds). If that
> is
> constant to within about 0.1 (or maybe 0.2) K, then the heating of the
> system
> is not likely to affect your results very much. Experimental temperature
> control in most protein experiments is no better than this anyway. Of
> course,
> this is only a heuristic argument, not a rigorous one.
>
> ...regards....dac
>
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-- 
mvh Lars Skjærven
Institutt for Biomedisin
Universitetet i Bergen

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