# Distance restraints for multiple copies of same peptide

**URL:** <https://gromacs.bioexcel.eu/t/distance-restraints-for-multiple-copies-of-same-peptide/9233>\
**Category:** User discussions\
**Created:** [May 27, 2024, 1:08pm UTC](https://gromacs.bioexcel.eu/t/distance-restraints-for-multiple-copies-of-same-peptide/9233 "2024-05-27T13:08:04Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![abhinav.sri89](https://avatars.discourse-cdn.com/v4/letter/a/e19adc/32.png) [@abhinav.sri89](https://gromacs.bioexcel.eu/u/abhinav.sri89)\
**Post date:** [May 27, 2024, 1:08pm UTC](https://gromacs.bioexcel.eu/t/distance-restraints-for-multiple-copies-of-same-peptide/9233/1 "2024-05-27T13:08:04Z")

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GROMACS version: 2023  
GROMACS modification: Yes/No  
Here post your question

Dear Gromacs Community,

I have a peptide sequence (named P5) from which I created a cylindrical structure using 6 P5 structures. I generated an initial coarse grained (CG) system consisting of POPE, POPG and CDL0 lipids with this cylindrical configuration of P5s using CHARMM-GUI. Since I had 6 individual same peptides, the CHARMM-GUI generated 6 individual itp files.  
During the NPT simulations, the peptides are not able to maintain their cylindrical configuration. So, I tried applying distance restrain. Following was the command I used:

gmx genrestr -f NEUTRALIZED-P5.gro -n index.ndx -disre -o restraint.itp

I copy and pasted the [distance\_restarint] parameters from restraint.itp in  
all individual itp files at the end.  
I am getting the following error:

NMR distance restraints with multiple copies of the same molecule are  
currently only supported with ensemble averaging. If you just want to restrain  
distances between atom pairs using a flat-bottomed potential, use a restraint  
potential (bonds type 10) instead.

Any suggestions would be highly appreciated.

Thanks in advance !

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<div class="post-metadata">

**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [May 28, 2024, 11:54am UTC](https://gromacs.bioexcel.eu/t/distance-restraints-for-multiple-copies-of-same-peptide/9233/2 "2024-05-28T11:54:59Z")

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I’d suggest following the advice given in the error output, use a restraint potential by adding a new bond (of type 10) to the itp files. See [https://manual.gromacs.org/current/reference-manual/functions/restraints.html#distance-restraints](https://manual.gromacs.org/current/reference-manual/functions/restraints.html#distance-restraints) and [https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html#id36](https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html#id36) for more information.