Molecular Dynamics with Helical Periodic Boundary Conditions

Download program and example

Note:

  • highly experimental software
  • no support, no guarantee
  • adapted version of Tinker 6.2
  • works for the Amber99 only
  • works with Lenard-Jones/point charge electrostatic potential only
  • implemented also for bond, angle, torsion angle and improper torsion energy terms
  • NVT simulations were tested only
  • parallel compilation and run possible (#PROC option)
  • some options are described in HPBC-options.doc, see also cross.i and rtwist.f source files

    Usage:

    1. tar -xvzf HPBC.tgz
    2. cd HPBC/tinker6.2bamdOMP_s92/source
    3. linuxparallel/compile.make
    4. linuxparallel/library.make
    5. linuxparallel/link.make
    6. linuxparallel/rename.make
      (see windowsparallel etc for windows/cygwin versions)

      (example computation):
    7. cd ../../pro9_94
    8. ../tinker6.2bamdOMP_s92/bin/minimize pro amber99 1
    9. ../tinker6.2bamdOMP_s92/bin/dynamic pro amber99 1000 1 0.1 2 298
      etc ..


    (back)