Handling D-Amino Acids in MDP File for GROMACS Simulations

User discussions
1

GROMACS version: 2024.4
GROMACS modification: Yes/No

I run molecular dynamics (MD) simulations for peptides containing D-amino acids and L-amino acids. However, in the MDP options, D-amino acids are not recognized as part of the “Protein” group in the TCL groups. Instead, they are identified by their specific residue names (e.g., DXXX ).

Therefore, when setting up the MDP file for the simulation, should I specify:
DXXX Protein Water_and_ions or could I group them with gmx make_ndx command and just pass in the options the grouped proteins name (DXXX_Protein Water_and_ions)

Or is there another recommended approach to include D-amino acids correctly?

2

What is the purpose of specifying these separate groups in the mdp file? If it is for thermostat purposes, I think in general one should never put the same molecule - defined by one topology - in different thermostatting groups (probably GROMACS itself would complain?), so I would prepare a group which contains the whole protein as you said. Hope someone with more experience than me in simulating D/L amino-acids can confirm.

4

Thank you!