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 <vvcha...@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 <pmcho...@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. > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
