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jewettaij / moltemplate

A general cross-platform tool for preparing simulations of molecules and complex molecular assemblies
http://www.moltemplate.org
MIT License
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"barr" pressure units? #100

Open zhuwenli0723 opened 5 months ago

zhuwenli0723 commented 5 months ago

In example “https://github.com/jewettaij/moltemplate/tree/e8dd1ce3bbeb98124fd37b3140e7d94f967608ac/examples/all_atom/force_field_OPLSAA/ethylene%2Bbenzene” (and this is the first example I read).. The generated “system.in.init” indicated that the unit is the “real”, so the pressure unit should be “atmospheres”. However, in the “run.in.npt”:

# Run a short simulation using a Langevin thermostat (for improved stability).
fix fxlan all langevin  300.0 300.0  120  123456  # temp: 300 K
fix fxnph all nph  iso 150.0 150.0 1000.0   # pressure: 150 barr

It uses the “barr” as the pressure unit. Should this be a mistake or is there something I am missing? Thank you so much and your great work!

zhuwenli0723 commented 5 months ago

oh, I got it.1 bar~=0.9869 atm...

jewettaij commented 3 months ago

Hi zhuwenli0723. Thanks for the correction, and sorry for the sloppiness. (I also misspelled "bar".) There's a lot of comments in these examples that need to be cleaned up. When I get a chance to update these examples, I'll include this correction as well ("barr"->"atm").

jewettaij commented 3 months ago

I'll close it once I've updated the examples.