Hello, A new project on the LCRC cluster has been requested. Please forward the information on to the LCRC Allocation sub-committee. Applicant's name: Yao Fan Applicant's institution: ANL Applicant's division: BIO Project Name: MCSG_MD Project title: Molecular dynamics simulations on protein structure determined at MCSG Associated funding: NIH, DOE Other Systems: Surveyor Science: EsxB is an antigenic protein secreted by Bacillus anthracis that plays an important role in host-pathogen interactions. Our group has determined high-resolution crystal structures of this protein and several mutants. Interestingly, this protein exhibits structural polymorphism, being able to adopt different conformations with minor perturbations from the environment, which may have profound biological implications. We want to investigate the free energy change between the different conformers and how different mutations affect the free energy landscape. Project description: We plan to run molecular dynamics simulations with NAMD. The size of the system is about 80000 atoms, including all explicit solvent molecules. Good scalability of the NAMD code has been tested and established on various platforms. For a total number of 200 nanoseconds' simulation time, which should be sufficient for free energy calculations, approx. 200000 core hours are needed. Project URL: Requested allocation: 250000 Justification: The requester has used 0 hours of their initial startup project. In addition to approving an initial amount, please specify a Category and Subcategory for this project. For a list of the current selection of approved categories, please see: https://wiki.lcrc.anl.gov/wiki/Processes/Categories Once the Allocation committee has approved the project, please go to the Project Management page to create it: https://accounts.lcrc.anl.gov/projects.php Thank You, The LCRC Accounts System