Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius!

From: Vijay Manickam Achari <vjrajamany.yahoo.com>
Date: Wed, 26 Dec 2012 03:10:44 +0000 (GMT)

Dear Case,

Thanks for your kind response.

Well I have small curious to know if there is any way to make the box size to increase in Z direction. Means reduce and fix the box size in X adn Y direction and increase the Z direction length, apart from suggested ideas (like reduce cut-off radius and make skinnb=1) ?

Regards
 
 
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com


________________________________
 From: David A Case <case.biomaps.rutgers.edu>
To: Vijay Manickam Achari <vjrajamany.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Monday, 24 December 2012, 22:21
Subject: Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius!
 
On Mon, Dec 24, 2012, Vijay Manickam Achari wrote:
>
> I am trying to simulate only water molecules in a box for 100 ns. I am
> using 1445 water molecules in a box size 50.499  43.396  20.071 and
> the parameter input file I use is as below:
>
> After 38 ns the simulation terminates saying "ERROR:   max pairlist
> cutoff must be less than unit cell max sphere radius!" in output file.

Your box is too small in the z-direction.  Basically, twice the cutoff (which
in your case is 9) plus skinnb (which defaults to 2, I think, but check your
output file) has to be less than the smallest box dimension (which is 20.07).
So you just barely qualify at the beginning.  If you get a fluctuation
in volume that reduces the z-length even slightly, you will trigger this
error.

So, you need to either make the cutoff smaller, or the box bigger.  You might
be able to get away with setting skinnb to 1.0.  That will slightly slow down
the calculation (not by much, I think) and you might not have to make any
other changes.

...dac


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Received on Tue Dec 25 2012 - 19:30:03 PST
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