Re: AMBER: simulating a crystal using the unit cell

From: David A. Case <>
Date: Thu, 14 Aug 2003 08:40:42 -0700

On Thu, Aug 14, 2003, Sarah Wittkopp wrote:
> I am trying to simulate a crystal, where all atoms are not contained in
> one unit cell. As a result, since the simulation is periodic I thought
> the atoms outside of the box would be imaged in the other side. I think
> the problem lies in that one cannot image all molecules in the unit cell.

It's not clear what kind of crystal you are considering. There are three
principal limitaions in sander:

a. You must have a molecular crystal: only non-covalent interactions between
unit cells are allowed. I can't tell if this is relevant to your phrase
"all atoms are not contained in one unit cell".

b. The direct sum calculation uses a minimum-image convention. Hence, the
size of the shortest dimension of the unit cell must be more than twice the
cutoff + skin; in practice, this means that unit cells less than 18 Ang.
are not supported.

c. One can only simulate unit cells, that is, symmetry relations between
molecules in different asymmetric units in the same unit cell are not

..hope this helps....dac

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            |
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Received on Thu Aug 14 2003 - 16:53:01 PDT
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