VMD-L Mailing List

From: Dudo (dudomail_at_gmail.com)
Date: Mon Feb 03 2014 - 21:44:29 CST

you may unwrap easily as dx = dx - nint(dx/Lbox)*Lbox, standard algorithms
for MSD calculations implement it.
check the book by Frenkel and Smith: Understanding molecular simulation

On Tue, Feb 4, 2014 at 2:04 AM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> Hi Juita,
>
> If your MD engine wraps, and enough particles go from one side of the
> periodic boundary to the other, your diffusion constants will be way
> off. Over the short term, the diffusion constant should be too high, as
> particles appear to teleport across periodic boundaries despite not
> moving very far along your real coordinate system (they are "wrapped"
> into the periodic image nearest to the origin). Over the longer term,
> with wrapping turned on, the maximum displacement any particle could
> experience is proportional to the box-size, so your diffusion constant
> will approach zero as time progresses. This should be easy to check, as
> then your MSD would no longer increase linearly with time, but rather
> plateau at some value. This is something you'll need to look into more
> deeply, and perhaps do a test with a simpler system that you know the
> answer to in order to track down what exactly is happening, as I suspect
> DFTB is doing something you aren't expecting it to.
>
> Good luck!
> -Josh
>
> On 02/03/2014 06:49 PM, . Juita wrote:
> > Dear Josh,
> >
> > I am so sorry for late reply. I think that I missed your email.
> > Thank you so much for your information.
> > Yes, so far I know, diffusion coefficients are normally reported from QM
> molecular dynamics studies.
> > You are right about long simulations. I am still continuing running the
> simulation until ns level. However, I think there is something wrong with
> the calculation which is not caused by long simulations as the
> self-diffusion coefficient values are 2 orders of magnitude lower.
> >
> > - I have double checked the units for both space and time and they are
> right. The trajectories are in Angstrom. I specified the timestep as 1
> femtosecond and MD restart frequency is 100 so that the time between frame
> is 100 fs.
> > - Yes, this is a periodic system. I am wondering if wrapping means the
> coordinates outside the specified box size. If there is a wrapping, do you
> think the diffusion constants can be far away (2 orders of magnitude
> difference) from the correct value?
> >
> > Thank you so much for your assistance.
> > Best regards,
> > Juita
> >
> >
> > ________________________________________
> > From: Josh Vermaas <vermaas2_at_illinois.edu>
> > Sent: 31 January 2014 01:12
> > To: . Juita; vmd-l_at_ks.uiuc.edu
> > Subject: Re: vmd-l: self-diffusion coefficient from RMSD
> >
> > Hi Juita,
> >
> > Are diffusion constants usually reported from QM studies? In my
> > experience, short simulations (<1ns) tend to be in the regime where
> > things are settling down and the Einstein relation gives nonsensical
> > answers (atoms haven't had the time to change directions enough for it
> > to be a good random walker yet). Some other possible explanations:
> >
> > -Trajectory spit out by DFTB may not be in the units you or VMD expect
> > (No idea if this is true, but just looking at the docs quickly, DFTB
> > uses Bohr instead of Angstrom internally, so make sure you check the
> > units for both space and time!).
> > -Is this a periodic system? If so, have you checked wrapping? There
> > should be no wrapping.
> >
> > Your shortcut should in principle work, but it never hurts to check an
> > alternative formulation for determining diffusion, and keep in mind that
> > computational diffusion constants do not perfectly agree with literature
> > values in general (although 2 orders of magnitude is a bit extreme).
> >
> > Good luck!
> > -Josh Vermaas
> >
> >
> > On 01/30/2014 03:21 AM, . Juita wrote:
> >> Dear VMD users,
> >>
> >> I am doing calculation of self-diffusion coefficient from the
> trajectories data obtained from DFTB+ simulation. I am wondering whether I
> do the correct calculation. I utilise VMD to calculate and plot the RMSD,
> then squared it to get the plot of MSD (mean square displacement). The
> self-diffusion coefficient is estimated from the slope of MSD vs time plot
> using Einstein relation. However, I get the value 100 times less compared
> to the literature value. I would appreciate any assistance for this problem.
> >>
> >> Thank you so much for your assistance.
> >> Best regards,
> >> Juita
>
> 

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