AMBER Archive (2005)

Subject: Re: AMBER: How to simulate a crystal structure?

From: David A. Case (case_at_scripps.edu)
Date: Wed Oct 12 2005 - 10:17:35 CDT

On Tue, Oct 11, 2005, Chunhu Tan wrote:
>
> I want to simulate a crystal structure, but its unit cell is not
> rectangular ( Beta \= 90). So, can I set such a box in Leap and run a
> simulation with PMEMD? If yes, how to do that?

It is possible to do crystal simulations of unit cells, but you have to do a
lot "by hand", since LEaP does not automate this process.

First, you need to construct initial coordinates. This is not trivial, since
typically many solvent molecules are missing from X-ray structures, and these
have to be filled in, but you don't know in advance how many there are, or
where they should be.

Second, you would just edit the final line of the inpcrd file to put in the
unit cell dimensions and angles that you want.

This is not a task for a novice. Maybe other readers of the list will have
some good suggestions about how to get things started. (Once you have a good
set of initial conditions, actually carrying out the simulation is now
different than for liquid-state simulations.)

...good luck...dac
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