From: Z.Y.Qiu (luoyuan126_at_gmail.com)
Date: Thu Mar 28 2013 - 07:51:31 CDT

Hi,everyone. Now I want to calculate root-mean-square thermal displacement
to check whether the nanopartical
in my simulation is liquid or not.However, I found RSMD in Analysis of
Extension in VMD is short for root
mean square deviation (
http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.1/ug/node198.html ) which has
a different definition of root-mean-square thermal displacement which is
defined as:
Sqrt( Avg (Sum ( ri(t+dt) -ri(t) ) )
Do you know there is a script to calculate root-mean-square thermal
displacement??
Best wishes!
03/28/2013