AMBER: MD simulation : problem

From: sachin patil <>
Date: Fri, 9 Jul 2004 22:08:15 -0700 (PDT)

 While running the MD simulations on my system, I was
getting an error message-
 NB pairs 397 8996882 exceeds capacity ( 9000000)....
That means the density of the waterbox is increasing.
So I increased the MAXPR parameter to 120,000.
 And by increasing the MAXPR, I have allowed the
density to go as high as it can.
 Now my problem is that, how does this increase in
density affect my simulations. I am using a cuttoff of
999.0. And I have a system of 657 residues. Is ok to
let the density to increase or to work at a lower

Any help and comments would be highly appreciated !
Thanks in advance.

Sachin Patil
Dept.of Medicinal & Biological Chemistry
University of Toledo, Toledo,
Ohio, 43606

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Received on Sat Jul 10 2004 - 06:53:01 PDT
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