Input files for 2D REChgT simulation of 3NHH

Reference: Enhanced Sampling of Buried Charges in Free Energy Calculations Using Replica Exchange with Charge Tempering. Xiaorong Liu and Charles L. Brooks, III. J. Chem. Theory Comput. 2024, 20, 3, 1051–1061

File description

toppar_c36_jul21/: CHARMM36m force field related topology and parameter files

input_files/: Input files and scripts to run 2D REChgT simulation of 3NHH

Simulation software

pyCHARMM: It needs to be compiled with BLaDE, skip mpi

How to run this example simulation?

# activate the Python environment where pyCHARMM is installed, for example,
conda activate pyCHARMM

cd input_files/3nhh/
sh run.sh

Note that in this example, SLURM is used. Therefore, it's necessary to modify file run_rest_ex2d.slurm in input_files/3nhh/ to request appropriate resources (e.g., partition, number of GPUs per node).

Also, we may need to pay attention to the "mpirun" command in run_rest_ex2d.slurm (line 56). Depending on the version of mpirun, the syntax may need to be slightly modified.