AMBER Archive (2004)

Subject: Re: AMBER: Lennard-Jones particle simulation

From: Thomas E. Cheatham, III (
Date: Wed Aug 25 2004 - 15:05:58 CDT

> 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.

Maybe the lattice conformation is not stable under NPT, i.e. that at 300K
it wants to melt. You have to be careful to have a good balance with the
LJ particles. I would suggest either increasing the well depth or running
at higher pressure with a long relaxation time. You could also try
running the lattice in vacuum to see if it still falls apart (my guess is
that it will). It seems unlikely to be an artifact of the pressure

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