VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 03 2017 - 13:20:57 CDT

Have you aligned your structures before measuring RMSD between them?

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Oct 03, 2017 at 09:38:44PM +0330, fatehi_at_eng.uk.ac.ir wrote:
> Dear VMD community
>
> I do a 30ns NpT simulation for Toluene . The total energy, average
> temperature, volume and average pressure are all oscillating in a
> reasonable way and their average values are indeed the targets. but ,
> the RMSD curve vs time shows a continuous increased pattern. I need the
> simulation results after equilibrium state. On the other hand, I think
> 30ns is long enough for the system to reach equilibrium. Is this an
> indication of somethin wrong with the simulation? what might be the
> reason?
>
> Best Regards!
>
> 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/