AMBER Archive (2007)Subject: RE: AMBER: Defining BOX INFO during TLEAP
From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Jan 24 2007 - 14:09:30 CST
Dear
> 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
Ross
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|\oss Walker
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