This file shows a simple configuration file for alanin. It performs basic dynamics with no output files or special features.
# protocol params numsteps 1000 # initial config coordinates alanin.pdb temperature 300K seed 12345 # output params outputname /tmp/alanin binaryoutput no # integrator params timestep 1.0 # force field params structure alanin.psf parameters alanin.params exclude scaled1-4 1-4scaling 1.0 switching on switchdist 8.0 cutoff 12.0 pairlistdist 13.5 stepspercycle 20
This file is again for alanin, but shows a slightly more complicated configuration. The system is periodic, a coordinate trajectory file and a set of restart files are produced.
# protocol params numsteps 1000 # initial config coordinates alanin.pdb temperature 300K seed 12345 # periodic cell cellBasisVector1 33.0 0 0 cellBasisVector2 0 32.0 0 cellBasisVector3 0 0 32.5 # output params outputname /tmp/alanin binaryoutput no DCDfreq 10 restartfreq 100 # integrator params timestep 1.0 # force field params structure alanin.psf parameters alanin.params exclude scaled1-4 1-4scaling 1.0 switching on switchdist 8.0 cutoff 12.0 pairlistdist 13.5 stepspercycle 20
This file shows another simple configuration file for alanin, but this time with full electrostatics using PME and multiple timestepping.
# protocol params numsteps 1000 # initial config coordinates alanin.pdb temperature 300K seed 12345 # periodic cell cellBasisVector1 33.0 0 0 cellBasisVector2 0 32.0 0 cellBasisVector3 0 0 32.5 # output params outputname /tmp/alanin binaryoutput no DCDfreq 10 restartfreq 100 # integrator params timestep 1.0 fullElectFrequency 4 # force field params structure alanin.psf parameters alanin.params exclude scaled1-4 1-4scaling 1.0 switching on switchdist 8.0 cutoff 12.0 pairlistdist 13.5 stepspercycle 20 # full electrostatics PME on PMEGridSizeX 32 PMEGridSizeY 32 PMEGridSizeZ 32