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

[Jerry Binder]

Amazing! Thank you so much!

On Fri, Nov 24, 2017 at 5:22 AM, João Henriques <
joao.m.a.henriques at gmail.com> wrote:

> Hi,
>
> The PDB format is fixed, so it's not really a gromacs problem *per se*.
> Take a look at this
> <http://www.wwpdb.org/documentation/file-format-
> content/format33/sect9.html>
> :
>
> "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.
>
> J
>
>
>
> On Thu, Nov 23, 2017 at 10:01 PM, Jerry Binder <jerry.multiscale at gmail.com
> >
> wrote:
>
> > 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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