[gmx-users] .GRO Formatting

[Tsjerk Wassenaar]

Hey,

If the gro file was built with a non-gmx program, it may be that the
numbers indeed broke the format, which then needs to be fixed. In case you
write your own program, you want to use a statement like atid = atid %1e5
to make sure it doesn't go over five digits. Correcting the format is
possible, but may become a tiny bit nasty.

Cheers,

Tsjerk



On Thu, May 30, 2013 at 9:09 AM, Dr. Vitaly Chaban <vvchaban at gmail.com>wrote:

> In GRO file, the atom numbers do not really matter. Just use any number you
> like. It will work correctly.
>
> mdrun will renumber atoms from 99999, as it likes, automatically.
>
> Dr. Vitaly Chaban
>
>
>
>
>
>
> On Thu, May 30, 2013 at 4:57 AM, Phil <pmchoini at syr.edu> wrote:
>
> > I'm working on a .GRO file and have come across a formatting error.
> >
> > In the manual, it states that the spacing for each column in the .GRO
> file
> > is:
> >
> > residue number (5 positions, integer)
> > residue name (5 characters)
> > atom name (5 characters)
> > atom number (5 positions, integer)
> > position (in nm, x y z in 3 columns, each 8 positions with 3 decimal
> > places)
> > velocity (in nm/ps (or km/s), x y z in 3 columns, each 8 positions with 4
> > decimal places)
> >
> > In my .GRO file, the atom number exceeds 5 positions. How should I
> reformat
> > the .GRO file to account for this?
> >
> >
> >
> > --
> > View this message in context:
> > http://gromacs.5086.x6.nabble.com/GRO-Formatting-tp5008625.html
> > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> > --
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-- 
Tsjerk A. Wassenaar, Ph.D.