[gmx-users] more than 99,999 atoms in conf.gro

[Sikandar Mashayak]

Thanks Chandan it worked!


On Tue, Jul 15, 2014 at 8:56 AM, Chandan Choudhury <iitdckc at gmail.com>
wrote:

> Hi Sikandar,
>
> Did you try resetting your atom number to 1 as it reaches 100000?
> I hope this would resolve the issue.
>
> Chandan
>
>
>
> On Tue, Jul 15, 2014 at 3:43 PM, Sikandar Mashayak <symashayak at gmail.com>
> wrote:
>
> > Hi
> >
> > I am trying to run a simulation with more than 99,999 atoms in a conf.gro
> > file.
> > However, when I run grompp I get an error
> >
> > Fatal error:
> > Something is wrong in the coordinate formatting of file conf.gro. Note
> that
> > gro is fixed format (see the manual)
> >
> > As suggested in the online manual, I am using the following format to
> write
> > conf.gro by a Python script:
> > {0:5d}{1:5s}{2:5s}{3:5d}{4:8.3f}{5:8.3f}{6:8.3f}.
> >
> > Could anyone please suggest me how to resolve the issue?
> >
> > Thanks,
> > Sikandar
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>
> --
>
> --
> Chandan Kumar Choudhury
> National Chemical Laboratory, Pune
> India
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