[gmx-users] RE: Number of atoms limitation

Tandia, Adama TandiaA at Corning.com
Wed Jul 14 18:27:50 CEST 2004

Dear ALL,
I found the answer to my question:
How large systems can I simulate with GROMACS?

"It's only limited by your memory, and GROMACS is quite modest in its memory requirements. As an indication: a system of 12000 atoms takes about 10Mb of memory, and 6000 atoms about 5.5Mb (on a SGI O2), which comes down to just over 900 bytes memory use per atom in your system (your mileage will vary). Due to the fact that we initially developed GROMACS to run on our home-built parallel machine, with only 8Mb of memory per processor, the code is quite well optimized for memory use. To get an indication of scaling of GROMACS performance as a function of system size, have a look at the scaling benchmark page.

Note that the .gro format only support atoms numbers up to 99999, so it will loop once it reaches 100000 atoms. This is no problem in GROMACS since we don't use the atom number from the .gro file."

Adama Tandia
Modeling & Simulation
Corning INC
Corning, NY 14831 USA
Tel:  607 248 1036
Fax: 607 974 3405

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