VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Oct 06 2017 - 10:58:48 CDT

Is the trajectory wrapped to fit inside the periodic cell? MSD won't be
correctly measured if atoms are being rewrapped constantly and jumping
across the boundary, since diffusion should naturally spread your
solvent out slowly in all directions rather than flinging it to the
other side of the box.

-Josh

On 10/06/2017 12:39 AM, fatehi_at_eng.uk.ac.ir wrote:
>
> Thanks dear joshua. I decide to measure the self-diffusion coefficient
> of Toluene in 298k. The calculated value from MSD method has %74 error
> relative to reported value. I check the parameter file with other
> references and the data are right. Could you help me about this?
> what's your suggestion?
>
> Thanks for your attention
>
> > 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!
> >> >>
> >> >>
> >> >>
> >> >
> >> >
> >> >
> >>
> >
> >
> >
>