[gmx-users] THE max number of atoms in gromacs?

João Henriques joao.m.a.henriques at gmail.com
Thu Nov 23 22:22:56 CET 2017


The PDB format is fixed, so it's not really a gromacs problem *per se*.
Take a look at this

"A model cannot have more than 99,999 atoms. Where the entry does not
contain an ensemble of models, then the entry cannot have more than 99,999
atoms. Entries that go beyond this atom limit must be split into multiple
entries, each containing no more than the limits specified above."

You could go around this by writing your model in the gro format instead,
which allows you to go over 99.999 atoms by simply restarting the atom
numbering from 0 once you hit 100.000.


On Thu, Nov 23, 2017 at 10:01 PM, Jerry Binder <jerry.multiscale at gmail.com>

> Hello gmx-users:
> I build a large system with more than 10,000 atoms, however I cannot
> write info to pdb file correctly. The pdb file format in gromacs
> specify 5 positions for atom-id, and it will cause problem if not.
> Since I have to use rtp file and "pdb2gmx" command to generate
> conf.gro and topol.top file, a pdb file with >100000 atoms is needed.
> How can I do with it?
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