Re: [AMBER] Query: ABMD

From: case <>
Date: Mon, 6 Dec 2010 07:39:42 -0500

On Mon, Dec 06, 2010, Kshatresh Dutta Dubey wrote:
> I have already simulated many small complexes using plain molecular
> dynamics. But, as i know, Amber is restricted for systems < 100,000 atoms.

This is not correct. We test Amber on systems several times this large, and
have some test cases with more than a million atoms.

> When i am using solvation box for a protein in trimeric form, the number of
> atoms exceeds 200,000 which is causing some errors in coordinate
> preparation. Here, i am interested in simulation in trimeric form. So, is
> there any idea to run simulation for this system??

We would need to know more about the "errors in coordinate preparation."


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Received on Mon Dec 06 2010 - 05:00:03 PST
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