RE: AMBER: Defining BOX INFO during TLEAP

From: Ross Walker <>
Date: Wed, 24 Jan 2007 12:09:30 -0800


> Thus I got following XYZ dimensions for my system:
> x = 132.2520008085
> y = 112.1080012323
> z = 75.430001914511
> Now, as the atom diameters are not calculated in VMD, so do you
> recommend adding 5 A in each dimension (or may be less like 2 or 3 A)
> for making a periodic box around the system

The beauty of computer simulation is that you rapidly can test a hypothesis
quickly and safely. Unlike in the lab where you don't know how much acid to
use so you figure you'll just chuck a load in hope it doesn't blow up in
your face. On a computer you can do this without worry.

Hence I would suggest that you simply try it with 2 angstroms, see if the
system is stable and see if it equilibrates. When you start the MD you'll
know very quickly if you have clashes at the edges of the box as you will
get extremely high VDW energies. If the simulation isn't stable and you
can't equilibrate out the problems with a constant pressure run then try
making the box bigger and repeat.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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Received on Sun Jan 28 2007 - 06:07:11 PST
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