Re: Using PBC tools for a cubic and a rectangular box

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Mar 27 2018 - 09:18:17 CDT

I can't say for sure. Also, I haven't tried with NetCDF files, although
they may work because molfile does support unit cell I/O.

For sure the fact that a DCD file was created with NAMD is not sufficient
to know whether it'll work: it depends on the value of DCDUnitCell, and on
the presence of PBCs. NAMD sets internally a { 1 1 1 90 90 90 } unit cell
when PBCs are not enabled to avoid divisions by zero, but this may end up
in unexpected behavior once the files are loaded in VMD.

Giacomo

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