This file shows a simple configuration file for alanin. It performs basic dynamics with no output files or special features.
timestep 0.5 numsteps 10000 cwd /scratch # Specify a working directory structure alanin.psf parameters alanin.params coordinates alanin.pdb exclude scaled1-4 1-4scaling 0.4 outputname output margin 1.0 stepspercycle 10 temperature 300.0 switching on switchdist 7.0 cutoff 8.0 pairlistdist 9.0
This file is again for alanin, but shows a slightly more complicated configuration. A coordinate trajectory file and a set of restart files are produced every ten timesteps. Langevin dynamics are also active in this configuration.
timestep 0.5 numsteps 10000 structure alanin.psf parameters alanin.params coordinates alanin.pdb exclude scaled1-4 1-4scaling 0.4 outputname output margin 1.0 stepspercycle 10 temperature 300.0 switching on switchdist 7.0 cutoff 8.0 pairlistdist 9.0 DCDfile alanin.dcd DCDfreq 10 restartname alanin.restart restartfreq 10 langevin on langevinTemp 300.0 langevinCol O
This file shows another simple configuration file for alanin, but this time with full electrostatics using DPMTA.
timestep 0.5 numsteps 10000 cwd /scratch # Specify a working directory structure alanin.psf parameters alanin.params coordinates alanin.pdb exclude scaled1-4 1-4scaling 0.4 outputname output margin 1.0 stepspercycle 10 temperature 300.0 switching on switchdist 7.0 cutoff 8.0 pairlistdist 9.0 # DPMTA parameters FMA on FMAMp 8 FMALevels 3 FMAFFT on FMAFFTBlock 4