VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Oct 05 2017 - 11:47:11 CDT

Absolutely nothing is wrong with the simulation (probably). It sounds
like your solvent is toluene, whereas the RMSD trajectory tool is meant
for solute types of things. If you measured the RMSD of water in typical
aqueous simulations, the RMSD would also go up.
-Josh

On 10/04/2017 11:22 PM, fatehi_at_eng.uk.ac.ir wrote:
>
> thanks Jashua for your attention. RMSD of Toluene. I aligned it first
> by RMSD trajectory tool of VMD, but it increses.what's wrong with my
> simulation?
>
> > RMSD of what, exactly? If it is toluene, I'd totally expect it to
> > increase unless you aligned it first, since toluene will continue to
> > diffuse over time, which will increase the RMSD as the simulation
> > progresses.
> > -Josh
> >
> > On 10/03/2017 01:46 PM, 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!
> >>
> >>
> >>
> >
> >
> >
>