Loading doc/src/Tools.txt +4 −4 Original line number Diff line number Diff line Loading @@ -76,10 +76,10 @@ Post-processing tools :h3 "pymol_asphere"_#pymol, "python"_#pythontools, "reax"_#reax_tool, "replica"_#replica, "smd"_#smd, "spin"_#spin, "xmgrace"_#xmgrace, "replica"_#replica :tb(c=6,ea=c,a=l) "xmgrace"_#xmgrace :tb(c=6,ea=c,a=l) Miscellaneous tools :h3 Loading Loading @@ -496,8 +496,8 @@ 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) This tool was written by (and is maintained by) Tanmoy Sanyal, while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com) :line Loading doc/src/temper.txt +7 −1 Original line number Diff line number Diff line Loading @@ -110,7 +110,13 @@ the information from the log.lammps file. E.g. you could produce one dump file with snapshots at 300K (from all replicas), another with snapshots at 310K, etc. Note that these new dump files will not contain "continuous trajectories" for individual atoms, because two successive snapshots (in time) may be from different replicas. successive snapshots (in time) may be from different replicas. The reorder_remd_traj python script can do the reordering for you (and additionally also calculated configurational log-weights of trajectory snapshots in the canonical ensemble). The script can be found in the tools/replica directory while instructions on how to use it is available in doc/Tools (in brief) and as a README file in tools/replica (in detail). The last argument {index} in the temper command is optional and is used when restarting a tempering run from a set of restart files (one Loading Loading
doc/src/Tools.txt +4 −4 Original line number Diff line number Diff line Loading @@ -76,10 +76,10 @@ Post-processing tools :h3 "pymol_asphere"_#pymol, "python"_#pythontools, "reax"_#reax_tool, "replica"_#replica, "smd"_#smd, "spin"_#spin, "xmgrace"_#xmgrace, "replica"_#replica :tb(c=6,ea=c,a=l) "xmgrace"_#xmgrace :tb(c=6,ea=c,a=l) Miscellaneous tools :h3 Loading Loading @@ -496,8 +496,8 @@ 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) This tool was written by (and is maintained by) Tanmoy Sanyal, while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com) :line Loading
doc/src/temper.txt +7 −1 Original line number Diff line number Diff line Loading @@ -110,7 +110,13 @@ the information from the log.lammps file. E.g. you could produce one dump file with snapshots at 300K (from all replicas), another with snapshots at 310K, etc. Note that these new dump files will not contain "continuous trajectories" for individual atoms, because two successive snapshots (in time) may be from different replicas. successive snapshots (in time) may be from different replicas. The reorder_remd_traj python script can do the reordering for you (and additionally also calculated configurational log-weights of trajectory snapshots in the canonical ensemble). The script can be found in the tools/replica directory while instructions on how to use it is available in doc/Tools (in brief) and as a README file in tools/replica (in detail). The last argument {index} in the temper command is optional and is used when restarting a tempering run from a set of restart files (one Loading
