NCSI: Multiscale QM/MM Simulations of Channel Proteins

Status	Completed
Mentor Name	Hai Lin
Mentor's XSEDE Affiliation	Research Allocation
Mentor Has Been in XSEDE Community	4-5 years
Project Title	Multiscale QM/MM Simulations of Channel Proteins
Summary	Channel proteins are membrane proteins that facilitate the moving of ions across membranes, and they perform a wide range of functions that are vital to cell growth, replication, and movement. Here, we develop and apply highly accurate and efficient QM/MM methods for multiscale simulations of critical channel proteins in order to gain insights into their acting mechanisms and underlying dynamics.
Job Description	Student will construct models of Hv1 proton channel proteins, equilibrate the model systems using classical MD, carry out combined QM/MM dynamics simulations of the proton migration, visualize the trajectories, and analyze the data. Computer programs to be used including NAMD, GROMACS, Gaussian, and our in-house QM/MM codes. The students need to write codes in Python or Fortran for specific tasks including for machine learning tasks.
Computational Resources	Comet
Contribution to Community	The project will contribute to the understanding of specific scientific problems as well as the training of next-generation researchers in computational sciences.
Position Type	Intern
Training Plan	Students should have working knowledge of MM, QM, and QM/MM calculations, are familiar with Linux operating system and HPC system, and have Python or Fortran coding experiences. The student will be trained in multiscale simulation algorithms and relevant programs including our in-house QM/MM codes.
Student Prerequisites/Conditions/Qualifications	Knowledge in biochemistry and statistics is helpful.
Duration	Semester
Start Date	06/01/2021
End Date	08/07/2021