AMBER Archive (2003)

Subject: Re: AMBER: Compiling AMBER, ie, number of atoms limit

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Thu Oct 09 2003 - 16:30:02 CDT

Hello,

There may be several lurking problems with large systems.
In Amber 7 the NATOM format is I6 (it's I5 in Amber 6),
suggesting a limit of 999999. But in recent threads
Bob Duke and Tom Darden indicated that troubles may occur
at substantially fewer atoms, perhaps > 333333.
You can find those Reflectors via google searches:
more than 100,000 atoms site:structbio.vanderbilt.edu
atom number mismatch in coord and topology site:structbio.vanderbilt.edu

On the other hand Amber 7 is known to work with,
see benchmarks/rt_polymerase:
     NATOM = 141154 NRES = 42245
 Number of triangulated 3-point waters found: 41189

Scott

On Thu, 9 Oct 2003, franck wrote:

> Dear Amber users,
>
> I would like to re-compile AMBER in order to deal with a higher number
> of atoms (MD with SANDER). Increasing the number of atoms will increase
> too the number of interaction.. So I imagine that I have to change, not
> only NATOM parameter but some others. Could anyone tell me which are the
> parameters to check and to change for this purpose ?
>
> I thank you for your help,
>
> Chevalier Franck
>
>

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