From: John Stone (
Date: Tue Oct 03 2017 - 13:20:57 CDT

Have you aligned your structures before measuring RMSD between them?

  John Stone

On Tue, Oct 03, 2017 at 09:38:44PM +0330, 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!

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