Loading doc/src/Tools.txt +15 −14 Original line number Diff line number Diff line Loading @@ -486,6 +486,21 @@ README for more info on Pizza.py and how to use these scripts. :line replica tool :h4,link(replica) The tools/replica directory contains the reorder_remd_traj python script which can be used to reorder the replica trajectories (resulting from the use of the temper command) according to temperature. This will produce discontinuous trajectories with all frames at the same temperature in each trajectory. Additional options can be used to calculate the canonical configurational log-weight for each frame at each temperature using the pymbar package. See the README.md file for further details. Try out the peptide example provided. This tool was written by Tanmoy Sanyal, while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com) :line reax tool :h4,link(reax_tool) The reax sub-directory contains stand-alone codes that can Loading Loading @@ -551,17 +566,3 @@ See the README file for details. These files were provided by Vikas Varshney (vv0210 at gmail.com) :line replica tool :h4,link(replica) The tools/replica directory contains the reorder_remd_traj python script which can be used to reorder the replica trajectories (resulting from the use of the temper command) according to temperature. This will produce discontinuous trajectories with all frames at the same temperature in each trajectory. Additional options can be used to calculate the canonical configurational log-weight for each frame at each temperature using the pymbar package. See the README.md file for further details. Try out the peptide example provided. This tool was written by Tanmoy Sanyal, while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com) tools/README +1 −0 Original line number Diff line number Diff line Loading @@ -38,6 +38,7 @@ polybond Python tool for programmable polymer bonding pymol_asphere convert LAMMPS output of ellipsoids to PyMol format python Python scripts for post-processing LAMMPS output reax Tools for analyzing output of ReaxFF simulations replica tool to reorder LAMMPS replica trajectories according to temperature smd convert Smooth Mach Dynamics triangles to VTK spin perform a cubic polynomial interpolation of a GNEB MEP vim add-ons to VIM editor for editing LAMMPS input scripts Loading Loading
doc/src/Tools.txt +15 −14 Original line number Diff line number Diff line Loading @@ -486,6 +486,21 @@ README for more info on Pizza.py and how to use these scripts. :line replica tool :h4,link(replica) The tools/replica directory contains the reorder_remd_traj python script which can be used to reorder the replica trajectories (resulting from the use of the temper command) according to temperature. This will produce discontinuous trajectories with all frames at the same temperature in each trajectory. Additional options can be used to calculate the canonical configurational log-weight for each frame at each temperature using the pymbar package. See the README.md file for further details. Try out the peptide example provided. This tool was written by Tanmoy Sanyal, while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com) :line reax tool :h4,link(reax_tool) The reax sub-directory contains stand-alone codes that can Loading Loading @@ -551,17 +566,3 @@ See the README file for details. These files were provided by Vikas Varshney (vv0210 at gmail.com) :line replica tool :h4,link(replica) The tools/replica directory contains the reorder_remd_traj python script which can be used to reorder the replica trajectories (resulting from the use of the temper command) according to temperature. This will produce discontinuous trajectories with all frames at the same temperature in each trajectory. Additional options can be used to calculate the canonical configurational log-weight for each frame at each temperature using the pymbar package. See the README.md file for further details. Try out the peptide example provided. This tool was written by Tanmoy Sanyal, while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com)
tools/README +1 −0 Original line number Diff line number Diff line Loading @@ -38,6 +38,7 @@ polybond Python tool for programmable polymer bonding pymol_asphere convert LAMMPS output of ellipsoids to PyMol format python Python scripts for post-processing LAMMPS output reax Tools for analyzing output of ReaxFF simulations replica tool to reorder LAMMPS replica trajectories according to temperature smd convert Smooth Mach Dynamics triangles to VTK spin perform a cubic polynomial interpolation of a GNEB MEP vim add-ons to VIM editor for editing LAMMPS input scripts Loading
