# PDB2GMX, structure too large

**URL:** <https://gromacs.bioexcel.eu/t/pdb2gmx-structure-too-large/5498>\
**Category:** User discussions\
**Created:** [December 27, 2022, 11:44pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-structure-too-large/5498 "2022-12-27T23:44:15Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![mjgp](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mjgp/32/2070_2.png) [@mjgp](https://gromacs.bioexcel.eu/u/mjgp)\
**Post date:** [December 27, 2022, 11:44pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-structure-too-large/5498/1 "2022-12-27T23:44:15Z")

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GROMACS version:2022  
GROMACS modification: No

I want to simulate a filament that extends along the z-axis to the extent that the z-coordinate exceeds the number of fields in a PDB file. How can I handle such a structure?

Best,  
Matthew

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**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [January 10, 2023, 3:10pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-structure-too-large/5498/2 "2023-01-10T15:10:48Z")

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Hi,  
Maybe the solution discussed in the post below, works also in your case.

> [@Infinite DNA (across boundary conditions)](https://gromacs.bioexcel.eu/t/infinite-dna-across-boundary-conditions/1628):
>
> GROMACS version: 2021 GROMACS modification: No Hi fellow GROMACSers, I am trying to simulate an infinite DNA using periodic boundary conditions. I have used a process that I believe was suggested by @jalemkul in a previous version of the gromacs forum, but it is very likely that I misunderstood it. I first created generated a 12bp DNA pdb (Using this website: [Sequence to Structure](http://www.scfbio-iitd.res.in/software/drugdesign/bdna.jsp) . If there are better ways of doing this, please offer suggestions.) I then ran it through pdb2gmx to create a …

\Alessandra