VMD-L Mailing List

From: angad sharma (angadsharma54_at_gmail.com)
Date: Sun Jan 08 2023 - 03:00:11 CST

Dear amber users,
Is there a way by which we can do rmsfit of DNA and ions of the trajectory
at a time for the density map plot in VMD plugin.

I am doing of rmsfit of DNA of the trajectory and then calculating the
density map of ions around DNA. In this way, it works but when I increase
the isovalue in VMD, density distribution of ions around DNA takes
spherical shape upto some isovalue then it takes the form of box structure.

Is there a way to correct this?