[gmx-users] More than 99999 atom

Erik Lindahl lindahl at csb.stanford.edu
Thu Mar 11 20:34:01 CET 2004


No problem whatsoever. Actually, the PDB format is even worse since it 
only reserves four positions for the number.

We have "generalized" our treatment of input files by only checking 
that the atom number on a line is different from the previous one. 
Internally we always use larger sequential numbers if necessary. As you 
already noted we restart from 0 when writing output files.

The lowest current limitation is that the neighborlists are limited to 
2Gb in size, which happens way before the system reaches 2e9 atoms. 
This isn't a problem for normal simulations (especially not on 32-bit 
systems where you can only allocated 2Gb in the entire process anyway), 
but we're working on a way to split neighborlists when necessary.



On Mar 11, 2004, at 5:41 PM, Ing. Vojtěch Spiwok wrote:

> Dear gromacs users and developers
> Do you know if it is possible to simulate systems with
> more than 99999 atoms? When number exceedes it
> the numbering in gro file starts from 0 again.
> Thanks
> Vojtech Spiwok
> ICT Prague
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