prave_PreQ1_riboswitch

GROMACS and PLUMED codes to reproduce result in the draft Interrogating RNA-small molecule interactions with structure probing and AI augmented-molecular simulations The simulations and analysis are preformed on 3 system: PreQ1 without ligand (apo), PreQ1 with the cognate ligand (6e1w) and PreQ1 with the synthetic ligand (6e1u)

Usage

Files for the MD simulations can be found in the gromacs folder.

You can run gromp to generate the binary input file (.tpr).
For apo system, you can run:

gmx grompp -f md.mdp -c npt.gro -p topol.top -t npt.cpt -o md_0_1.tpr

For riboswitch with cognate or synthetic ligand, you can run:

gmx grompp -f md.mdp -c npt.gro -p topol.top -t npt.cpt -n index.ndx -o md_0_1.tpr

You can run mdrun to start the enhanced MD simulation:

gmx mdrun md_0_1 -plumed plumed.production.dat

The associated PLUMED files can be found in the production folders.

To calculate the C2-C2 distances, please refer to the files in the analysis folders.