Re: [AMBER] issues with pmemd

From: case <case.biomaps.rutgers.edu>
Date: Tue, 30 Mar 2010 14:23:19 -0400

On Tue, Mar 30, 2010, Ganesh Kamath wrote:
>
> I have a system size of 303.4454000 303.3504000 303.3644000 box size and it
> has 141000 atoms with water.

Something is badly wrong here. Your unit cell volume is way too big for a
system of 141,000 atoms. Roughly, that many atoms would occupy something
like 1.5 x 10^6 A^3, but your unit cell is 27 x 10^6 A^3. You will need to
re-visit the way you prepared the system.

....dac


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Received on Tue Mar 30 2010 - 11:30:04 PDT
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