AMBER: Problems simulating a big system

From: Jordi Camps <>
Date: Mon, 16 Jul 2007 13:55:55 +0200


I'm trying to run a MD simulation of a big system, and I'm getting some
trouble with Amber 9.
When I run the simulacion with sander (MPI version), the program crashes
after a few steps wthout giving further information. And when I try to
run the same input with pmemd, the software complaints about:
        | ERROR: nfft3 must be in the range of 6 to 256!
This parameter has not been defined, but it is likely to be around 400
because the box is 200x300x400 Angstroms.
Is there any real problem for this limit? Can I look for it in the
source code and change the upper limit without problems? Has someone
experience simulating big systems (750000 atoms) with sander? Any
suggestion about why it crashes?

Thank you very much!

Jordi Camps Puchades
Supercomputing research, support and development
Barcelona Supercomputing Center   | Instituto Nacional de Bioinformática
                                  |   GN6-MN UPC-BSC (                 |
Tel. : 934 137 602                | Tel. : 934 037 155
Fax  : 934 137 721                | Fax  : 934 037 157
c/ Jordi Girona, 29               | c/ Josep Samitier, 1-5
Edifici Nexus II, despatx 1B      | PCB, Edifici Modular, PBC32
E-08034 Barcelona                 | E-08028 Barcelona
Catalunya (Spain)                 | Catalunya (Spain)
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Received on Wed Jul 18 2007 - 06:07:21 PDT
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