Re: AMBER: minimum image convention mystery

From: David A. Case <>
Date: Sat, 16 Aug 2003 17:02:03 -0700

On Sat, Aug 16, 2003, Martin Mucha wrote:
> I have been trying to simulate binary mixture of Lennard-Jones
> particles in a periodic box, in the NVE ensamble. However, the energy
> did not conserve....

How big is the box, and how big is the cutoff you are using?

> I am using Amber 7, the same happens in Amber 6.
> time step is pretty reasonable for a LJ system, dt=0.01
> LJ parameters are those for Argon and Krypton.
> I calculate the neighbour list every step:
> nsnb=1
> no pme or other tricks:
> ew_type=0
> vdwmeth=0
> eedmeth=1
> use_pme=0
> nbflag=0
> wrapping the coordinates:
> iwrap=1
> (setting iwrap=0 will not change the problem)

This is certainly an unusal combination (for a code pointed at biomolecular
simulations!), and there is a chance somethings don't work together correctly.
Can you run a short simulation with just the default parameters, to see what
happens? Tom Cheatham had some problems with a system that had no charges
on any atoms...maybe he can chime in with his experience.

Two other ideas: try this with sander_classic from amber6: that uses a
completely different way of doing the non-bonded forces; and send us your
input files so that we can try to reproduce this.


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Aug 17 2003 - 01:53:00 PDT
Custom Search