On Tue, Jun 08, 2010, Ehsan Habibi wrote:
>
> I am doing a Simulation of a DNA (240-mer) using AMBER9.
This is probably not possible without modifying the Amber code, and
understanding a lot about what you are doing. First, do you really need
to simulate a 240 bp sequence? This is about 800 Ang. in lenght, which is a
seriously big system. You might try to see if pmemd will swallow this, or
if it makes it easier to expand the size of the grid. If that doesn't work,
you will probably have to study the code to figure out how to allow really
large box sizes.
....dac
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Received on Tue Jun 08 2010 - 08:00:04 PDT
