Distance restraints for multiple copies of same peptide

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1

GROMACS version: 2023
GROMACS modification: Yes/No
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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 !

2

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 and https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html#id36 for more information.