MD Simulations

A 50 ns MD simulation has been run with the open-like CFTR (PDB: 6MSM) in 1M KCl. The simulation system was built using CHARMM-GUI. The goal of the simulation was to see if a chloride ion can cross the narrowest part of the CFTR pore (bottleneck). In 6MSM, no conduction path (> 3.6 angstroms in diameter) was observed but a chloride ion might be able to wiggle through the dynamic bottleneck.

After the simulation, the following commands were used to center the CFTR protein in the simulation system:

1. module load cuda/9.2 gcc/7.3.0

2. source /home/yohei/Library/gromacs/versions/2019.4/cuda-9.2/gcc-7.3.0/threads/bin/GMXRC

3. gmx trjconv -f step7_production.trr -s step7_production.tpr -o 6msm-1M-KCl.xtc -center -ur compact -pbc cluster

(Choose the Protein for clustering and centering and the System for output)

4. gmx trjconv -f 6msm-1M-KCl.xtc -s step7_production.tpr -o output.xtc -center -ur compact -pbc mol

sftp (username)@bridges.psc.edu

>lcd (destination directory on your computer)

>cd (source folder on Bridges in your account)

>get step7_production.xtc