On Mon, Nov 18, 2002, Tod Pascal wrote:
> I'm running a simulation on a fairly large DNA molecule (92 base pairs).
> When I try to do some initial dynamics (5ps - 10000 steps) I get this
> error at the 1,000th step:
>
> * NB pairs 225 8999788 exceeds capacity ( 9000000) 0
>
> SIZE OF NONBOND LIST = 9000000
> EWALD BOMB in subroutine ewald_list
> Non bond list overflow!
> check MAXPR in sizes.h
>
You need to increase the size of MAXPR in sizes.h, and recompile. As a
pretty good guess, set
MAXPR = 0.3*natom*(cut+skinnb)**3
[If you can get access to an fortran90 compiler, you can set MEM_ALLOC in your
MACHINE file, then this will be done for you by the code. This ability
to dynamically allocate memory based on the size of the input is not available
with fortran77 compilers, of which g77 is probably the only remaining major
example. In particular, for Linux systems, intel makes an fortran90 compiler
(ifc) available for academic use, and there are several commercial fortran90
compilers available as well. Almost all Unix systems now come with fortran90
compilers....)
..hope this helps...dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Mon Nov 18 2002 - 16:27:37 PST
