VMD-L Mailing List

From: Liyu Jin (Leo) (liyu.jin_at_monash.edu)
Date: Sat Dec 01 2012 - 07:56:30 CST

Dear VMD users,

I was looking for the method to plot probability density map to visualize the probability of finding a particular kind of ion/atom around a selected molecule average over all the frames. And I found the Volmap Tool of VMD may be useful. But after some searching and reading I still cannot figure out how to use the Volmap tool to fit my purpose. To be specific:
1. On the GUI, "selection" should be the selected/surrounded molecule or the surrounding atoms?
2. "volmap type" should be the "density" ?
3. for "average combining all of the frames", will the tool convert the coordinates according to the orientational change in different frames of the selected "solute" molecule, so that the final isosurface shows the "solvent" ions' probability around the single oriented "solute" molecule ？

any help will much appreciated !

Cheers
Liyu Jin (Leo)