VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Oct 23 2019 - 14:35:24 CDT

Ahh, I see what happened. For the file formats I use, VMD reads in the periodic box information from the trajectory file, which lets VMD do the math internally to figure out a PBC-correct representation of atomic positions, and is why I've never set unit cell length when using the plugin. From the little snippet you sent along earlier, I'm not sure if that information is read in with your trajectory file. What is the output of something like:

package require pbctools; #Loads in a snazzy package
puts [pbc get] ; #This prints the current periodic box size for the active frame of the top molecule

If the first three numbers are 0, VMD doesn't know what the periodic box dimensions are. In this case, you'd either need to not use PBC when calculating your g(r) (not recommended), or tell VMD what the box dimensions should be for every frame. This depends on what you used to do the simulation, and what outputs you have.

-Josh

On 2019-10-23 13:24:10-06:00 Sarah Fowler wrote:

Joshua, thank you. Maybe I don't understand how the GUI works. I hope you're right that the box volume doesn't matter.
I thought that the box volume mattered because it is possible at the GUI to specify periodic boundary conditions (bottom left-hand corner). At the top left, there's a "Set Unit Cell." I assumed that the unit cell was required for correct recognition of the PBC. Are you saying that anything could be entered for the unit cell and the RDF will not be affected? Thank you.