Re: [AMBER] Do molecular dynamics in the limited space

From: Bill Ross <>
Date: Wed, 21 Apr 2010 09:59:39 -0700 (PDT)

> I would like to do molecular dynamics in the limited space, such as in
> the rectangular box with "20*20*100" or in the cylinder with the diameter
> of 20 A.

Cylindrical space is not supported.

Usually when there is a box, there is also a solvent, usually water.
The solvateBox command will build a box to enclose a given radius
from the solute. However the size will not be exact, and the radius
will be observed the same in eacxh dimension. Then the system must
be equilibrated at constant pressure to make the density correct.
See the demos for details.

If you want a molecule in vacuum in a box, you can try 'help setbox'
to see how to create a box, then after saveamberparm you can edit the
prmtop and inpcrd to expand the box to the dimensions you like.


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Received on Wed Apr 21 2010 - 10:00:04 PDT
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