VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Oct 03 2017 - 14:49:16 CDT

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!
>
>
>