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: Benoit Roux Applicant's institution: ANL Applicant's division: BIO Project Name: nachbac Project title: selectivity of the sodium channel Associated funding: NIH R01-GM062342 Other Systems: Science: Understanding quantitatively the microscopic factors giving rise to Na+ selective channels is mysterious. For a long while, we had only K+ selective channels (such as KcsA). Just recently, the X-ray structure of a Na+ selective channel was determined. It is related to the NachBAC channel (Na+ Channel from bacteria). Project description: The most informative strategy to address the issue of Na+ selectivity in NachBAC is to compute the multi-ion PMF corresponding to the microscopic process in question (Berneche and Roux, Nature 2001). In particular, the calculation of the PMF enables us to pin-point the location of the largest barrier opposing the passage of a single K+ ion relative to Na+ in the channel, thus explaining while the channel becomes selective from the free energy profile. We can carry those type of calculations using our new and highly scalable method called umbrella sampling with replica-exchange MD simulations. This is a competitive projects as others are racing to produce calculations. This is why our request is biggest at the early stage of the project. Project URL: Requested allocation: 1000000 Q1: 500000 Q2: 250000 Q3: 150000 Q4: 100000 Justification: The MD umbrella sampling with replica-exchange is a new method that was recently implemented by Wei Jiang. On BG we are able to run such computations up to 32 racks on similar systems. The scope of this project is smaller and on fusion, we plan to use the resource to carry out the calculation as efficiently as possible. The requester has used undetermined amount 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