Re: [AMBER] Fwd: About long simulation

From: Daniel Roe <>
Date: Wed, 16 Feb 2011 15:57:30 -0500


On Wed, Feb 16, 2011 at 3:08 PM, haris p <> wrote:
> Thanks for the quick reply. Why part of the DNA comes outside the truncated
> octahedron box when put iwrap = 1 without spliting in to two strands?

I believe the way that Sander wraps molecules based on whether the
geometric center of the molecule is outside the boundaries of the unit
cell. So if the geometric center of both DNA strands are at the edge
of the unit cell but not quite outside the boundaries, it may look
like the DNA is sticking out into nowhere. Again, this is just a
visualization artifact; the DNA strands are still interacting with
solvent on the opposite side of the unit cell.


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Received on Wed Feb 16 2011 - 13:00:02 PST
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