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How to use Protein_Area

Installation

Follow README.

Use as

python -m Protein_Area.ProteinArea -s TOPOLOGY -f TRAJECTORY -d SLICETHICKNESS

Pre-processing

We need a trajectory with the system centered on the membrane with the protein whole (and near the center). Do not remove rotation (i.e., do not superimpose). If you analyze multiple systems, ensure that they are all oriented in the same way in the membrane.

Example with GROMACS (actually centers on the protein, which should be sufficient)

#!/usr/bin/env bash
#SBATCH --job-name=center_on_sys
#SBATCH --output=center_on_sys.%j.out
#SBATCH --partition=compute
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=2
#SBATCH --mem=8G

set -euo pipefail

module purge
module load gromacs/2023.3/cuda12.3/gnu-11.4.0/avx/bare/64


gmx trjconv -s step7_production.tpr \
            -f step7_centererd2.xtc \
            -o step7_center_on_sys.xtc \
            -pbc mol -ur compact -center <<EOF
Protein
System
EOF

Running the analysis

#!/usr/bin/env bash
#SBATCH --job-name=area_V1
#SBATCH --output=slurm.%j.out
#SBATCH --partition=compute
#SBATCH --nodes=1
#SBATCH --ntasks=8
#SBATCH --mem=12G

set -euo pipefail

echo "Starting ProteinArea on step7_center_on_sys.xtc "
module purge

eval "$(mamba shell hook --shell bash)"
mamba activate proteinarea

output="Chol1_V1.npy"

python -m Protein_Area.ProteinArea.py \
    step7_production.tpr step7_center_on_sys.xtc \
    --output ${output} \
    --zmin 27 \
    --zmax 137 \
    --layer 0.5 \
    --backend multiprocessing \
    --workers ${SLURM_NTASKS} 

echo "Saved area to $output"
echo "Analysis complete!"