Re: [AMBER] cut value in minimisation

From: Jason Swails <>
Date: Fri, 21 Nov 2014 05:18:44 -0500

> On Nov 21, 2014, at 2:17 AM, Robin Jain <> wrote:
> Dear all,
> 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 .

The cutoff has no effect on the box size. In fact, the only thing that can change the box size is a constant pressure simulation (which is _supposed_ to change the box size). I would suggest just using 8 A or something close to that.

Why do you continue to think that your box size keeps changing due to different settings?

> Since i used 8 A value but the program
> still stop with an error, so please help me in this regard.

Change the setting causing an error so that the error doesn’t occur.

That is the best help anyone provide given this information. What was the exact error message you got? What was the input that you used? Did you google the error message to see if someone has encountered the problem before? What did you do to try and fix the problem?

Be specific, and give exact input and output, but only the parts that are actually relevant to reproducing and/or diagnosing your problem.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Nov 21 2014 - 02:30:03 PST
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