Re: [AMBER] AMBER Digest, Vol 1045, Issue 1

From: David A Case <case.biomaps.rutgers.edu>
Date: Sat, 22 Nov 2014 07:39:51 -0500

On Sat, Nov 22, 2014, Robin Jain wrote:

> If i use small cut value such as 6 Ang., Would the periodic boundary
> condition maintained or not. Because in a AMBER tutorial i have
> studied that the lower cut off may destroy the PBC.

Such values of the cutoff will certainly lead to bad results, but they will
not affect the fact that PBC's are maintained. It would be helpful if you
could point out the exact location in the tutorials where you found the
confusing statements -- we'd like to make these as helpful as possible.

If you are really convinced you need a 17.5 Ang box, use cut=8 and skinnb=1,
and you should be fine. But this is about the smallest size system that Amber
is able to use.

....dac


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Received on Sat Nov 22 2014 - 05:00:03 PST
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