# Running gmx editconf corrupts some of the crystal coordinates

**URL:** <https://gromacs.bioexcel.eu/t/running-gmx-editconf-corrupts-some-of-the-crystal-coordinates/4349>\
**Category:** User discussions\
**Created:** [June 23, 2022, 3:45pm UTC](https://gromacs.bioexcel.eu/t/running-gmx-editconf-corrupts-some-of-the-crystal-coordinates/4349 "2022-06-23T15:45:41Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![PSS67](https://avatars.discourse-cdn.com/v4/letter/p/ee59a6/32.png) [@PSS67](https://gromacs.bioexcel.eu/u/PSS67)\
**Post date:** [June 23, 2022, 3:45pm UTC](https://gromacs.bioexcel.eu/t/running-gmx-editconf-corrupts-some-of-the-crystal-coordinates/4349/1 "2022-06-23T15:45:41Z")

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GROMACS version: 2022.1  
GROMACS modification: No  
I am trying to simulate an amide crystal. In order to do this I need to use editconf to make a 4x4x4 unit cell box where each unit cell contains four molecules. So I have 64 unit cells of 4 molecules each. The command I use is:  
gmx editconf -bt triclinic -f $NAME.gro -o “$NAME”\_box.gro -box 3.844 2.608 2.896  
-angles 90 90 90 -pbc 90 90 90 -pbc &\> editconf.out  
I can see in PyMol that the starting coordinates are fine, but the resulting box coordinates for about a dozen or so molecule pairs is corrupted. What happens is that CH3 atom of the acetyl group which starts about 1nm away from the CH3 of the N-methyl group of a molecule in the next unit cell, moves (with its H-atoms) to about 0,05nm away from N-methyl CH3. So now, for these 12 (periodically related) molecule pairs, I get a bonded C-C group with 6 H-atoms each bonded to 2 C-atoms. I have generated boxes for a number of different amide crystals. but the is the first time I have encountered such strange behavior.  
If anybody has any idea of what might be going on I would be very happy to hear from them.