trajectories for GCMC

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1

Hi,

I have been running GCMC calculations. Has anyone looked at formats that would be good for reading “trajectory” data for variable numbers of particles into programs like VMD? I add/delete hexane and other small molecules into the system and find some nice results and the visualization works in my OpenGL tool for debugging the new simulations and watching what happens, but I’d want to process these trajectories later and it is a difficult problem.

Maybe Axel Kohlmeyer has a tool for this purpose in Topotools or other methods? We do NVT-MD/GCMC in LAMMPS and MC/GCMC in our own code (and now some C++ OpenMM stuff too for using GBSA and GBVI implicit solvation models) and so I would need a good way to analyze the data with variable # of particles… perhaps dummy particles would help? I don’t mind the larger trajectory sizes but there should be a solution here and I am willing to write some more code, we have tons at the moment.

Thanks,
Luke

2

short of modifying the dump classes in LAMMPS, you currently have the
following options:
- write a tool that adds suitable dummy atoms to dump files
- dump xyz trajectories and use topotools to read those (less dummy
atoms, but order of atoms is not preserved, so probably not what you
want) https://sites.google.com/site/akohlmey/software/topotools/topotools---documentation#TOC-readvarxyz-file-name-
- use the LAMMPSMAXATOMS environment variable with custom/atom style
dump files: https://sites.google.com/site/akohlmey/software/lammps-plugin
  (need to generate a suitable .psf file, or else added molecules will
not have proper names/types/elements)
- read each frame into a separate VMD molecule and use multimolanim (
http://www.ks.uiuc.edu/Research/vmd/plugins/multimolanim/ )
- don't use VMD

axel.