AMBER Archive (2004)

Subject: Re: AMBER: Lennard-Jones particle simulation

From: darden (darden_at_gamera.niehs.nih.gov)
Date: Wed Aug 25 2004 - 15:57:15 CDT

one more possibility---any chance the lennard-jones parameters are
confused between sigma; the point where lj curve crosses the x-axis and
energy increases steeply, and the position of minimum energy??
if amber is mistaking the two you will likely blow up

In case above is unclear--what I mean is the code that built the lattice
may be assuming the the lj distance parameter is sigma whereas amber
assumes that parameter refers to distance of minimum energy--in which case
amber will expand the system as soon as you let it
to check this possibility out try dividing the LJ distance parameter you
are using by sixth root of 2
just a possibility
Tom D
 On Wed, 25
Aug 2004, Guanglei Cui wrote:

> Dear all,
>
> Can anyone suggest me a good way to equilibrate a box of Lennard-Jones
> particles at 300K and 1atm starting with certain lattice conformation? I
> tried minimization and a long NVT MD. But as long as I switched to NPT,
> the system just blew up after some picoseconds. Thanks.
>
> Guanglei
>
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