1. Molecular Simulation at MCSR Brian W. Hopkins Mississippi Center for Supercomputing Research 9 October 2008

2. What We’re Doing Here Talk about molecular simulation procedures. Talk about available simulation programs. Discuss user simulation needs and program options.

3. Simulation: Anatomy of A Program Read in sim paramters, atomic coordinates and topology. Begin Timestepping –Apply periodic boundary conditions. –Build neighbor list. –Compute bonded forces. –Compute short-rang nonbonded forces. –Compute electrostatic forces. –Integrate forward in time. Write atomic positions, velocities and forces. Take data for statistical accumulators. –Repeat. End timestepping. Print restart data.

4. Program Anatomy: Read Control nafion #restart temperature 298.00 steps 200000 timestep 0.00050 ps ensemble nve evbconv 1e-6 movlp 1 cutoff 10.0 angstrom rvdw 9.0 angstrom delr 0.00 angstrom

5. Program Anatomy: Read Config hcl in water 2 1 2000000 0.001 21.5518556898 0 0 0 21.5518556898 0 0 0 21.5518556898 …… OW 7 15.994900 -0.820000 4.5231E-01 4.3198E+00 -6.6975E+00 4.7263E+00 3.4690E-01 -6.3309E+00 -1.9170E+04 5.2043E+03 -2.1576E+03 HW 8 1.007800 0.410000 5.1477E-01 5.3695E+00 -6.6887E+00 1.0886E+01 -6.6502E+00 2.6571E+01 -6.1635E+02 -8.2402E+03 2.6958E+03 HW 9 1.007800 0.410000 -5.5940E-01 4.0344E+00 -6.5708E+00 7.6145E+00 -7.4611E-01 -1.0319E+01 1.8438E+04 1.8167E+03 8.6264E+02 …

6. Program Anatomy: Read Topology UNITS kcal MOLECULAR TYPES 4 FLEXIBLE-TIP3P-Water NUMMOLS 332 atoms 3 OW 15.9949 -0.8200 HW 1.0078 0.4100 BONDS 2 harm 1 2 1059.162 1.012 harm 1 3 1059.162 1.012 ANGLES 1 harm 2 1 3 75.900 113.240 FINISH …… vdw 9 OW OW lj 0.155425 3.16549 OT OW lj 0.1238000 3.1420000 HT OW lj 0.0025115 1.5827460

7. Program Anatomy: Set up Cell