AMBER Archive (2008)

Subject: Re: AMBER: What's making my system lose total energy?

From: David Cerutti (dcerutti_at_mccammon.ucsd.edu)
Date: Tue Mar 18 2008 - 13:43:42 CDT

In fact, I tried setting nscm=0 and also the dsum_tol an order of
magnitude lower, but by this morning the energy loss was pretty much the
same. I set the SHAKE tolerance to 1.0e-6, so a full order of magnitude
lower rather than half its default value, and that seems to have finally
worked--the total energy is now stable. I actuallly had two systems I was
trying to do this for--the second had 136 glycerols and 1024 waters.

That second system was also lossing energy, though only about half as
severely; half as many glycerols, half as many SHAKE-constrained
hydrogens, half the rate of energy loss. (Water was constrained by SETTLE,
though I think I recall that pure water systems are also sensitive to the
SHAKE tolerance for some reason.) I don't know if anyone might find that
interesting...

Dave

On Mon, 17 Mar 2008, David Cerutti wrote:

> Heathen! Burn him!
>
> Yes, I mentioned at the coda to my query that I had looked very hard to make
> sure this system hard truly equilibrated, and have simulated it for many ns
> in NPT as well as NVT before beginning NVE dynamics. I suspected that the
> nscm may be slowly bleeding away energy; I think that my problems are solved,
> so thank you!
>
> Dave
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