AMBER Archive (2004)

Subject: Re: AMBER: Lennard-Jones particle simulation

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Wed Aug 25 2004 - 16:11:37 CDT

Thanks for all the replies from Dr. Cheatham, Dr. Simmerling, and Dr.
Darden. What I'm trying to do is to get LJ liquid. The starting
conformation is created by placing particles in their VDW contact
distance. I managed to relax it with one set of LJ parameters. It's
similar to what Dr. Cheatham suggested. I ran NVT MD at high temperature
and then cooled it over a long period of time at NPT to the desired
temperature. But as I reduced the VDW radius by 0.1 angstrom, it still
blew up.

Guanglei

Thomas E. Cheatham, III wrote:
>
>
> 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
> coupling.
>
>
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