From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Wed Feb 23 2011 - 14:21:51 CST

It would appear that there is a small problem with the namdenergy plugin. The gui allows for a stride entry to be made, however, it appears to be ignored when you receive the eventual energy/force plot. For example, I have 201 frames loaded in vmd and with a stride setting of 100 I still have 200 data points in the plot. This behavior is the same in vmd1.8.7.

In addition, it would also seem that a "protein and same residue as within 6 of resname blah" in the second selection is not supported. Only values of zero are reported in the final plot and data file. Is the plugin supposed to be able to accept this type of atom selection query?

Thanks
Brian Bennion
 

Biosciences and Biotechnology Division
Lawrence Livermore National Laboratory
7000 East Ave Livermore California 94550
phone:925-422-5722
fax:925-424-4334