VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon May 05 2008 - 16:19:47 CDT

It depends on how you do it. Are you using a script? One of the
tools? Either way, you can control what the reference is. If it's
still not clear, could you be more specific on how you're doing it
and include any relevant scripts, etc.?

On May 5, 2008, at 3:03 PM, snoze pa wrote:

> Dear NAMD users,
> I am using vmd to calculate the rmsd from my simulation. I have a
> question related to rmsd calculations. what is the rmsd values! Is it
> relative to minimized protein structure or to the original crystal
> structure? Thank you very much for your suggestions.
> s