Re: [AMBER] cut value in minimisation

From: David A Case <>
Date: Fri, 21 Nov 2014 07:26:26 -0500

On Fri, Nov 21, 2014, Robin Jain wrote:

> I am minimising my system in a cubic box of 17.58 A using sander. for
> this what value of cut must be used so that periodic boundary
> condition remain constant . Since i used 8 A value but the program
> still stop with an error, so please help me in this regard.

As Jason pointed out, providing the actual error message would be a great

Generally, the box size must be greater than 2*cutoff + skinnb, where skinnb
is a buffer region that allows the nonbonded list to be updated less
frequently. It's default is 2 Ang, which (I'm guessing!) is what is causing
your error.

You *could* reduce skinnb to 1 Ang. But 17.5 Ang is a very small box size for
Amber calculations. So you should also consider going to a bigger system.


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Received on Fri Nov 21 2014 - 04:30:02 PST
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