AMBER Archive (2004)

Subject: AMBER: MD simulation : problem

From: sachin patil (sachin_ppatil_at_yahoo.com)
Date: Sat Jul 10 2004 - 00:08:15 CDT

Hi,
 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
cutoff?

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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