Molecular Simulation at MCSR

Brian W. HopkinsMississippi Center for Supercomputing Research

9 October 2008

What We’re Doing Here

• Talk about molecular simulation procedures.

• Talk about available simulation programs.

• Discuss user simulation needs and program options.

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.

Program Anatomy: Read Control

nafion#restarttemperature 298.00

steps 200000timestep 0.00050 ps

ensemble nveevbconv 1e-6movlp 1

cutoff 10.0 angstromrvdw 9.0 angstromdelr 0.00 angstrom

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+03HW 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+03HW 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…

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

Program Anatomy: Set up Cell