VMD-L Mailing List

From: Chathurika Abeyrathne (c.abeyrathne_at_student.unimelb.edu.au)
Date: Tue Jun 28 2011 - 19:56:41 CDT

I loaded psf, pdb and dcd files to VMD and then I selected all the
molecules to obtain the total dipole moment.

I used NAMD to obtain the trajectory file. The simulation time is 81 ps. I
ran this 50 times and each time I obtained the total dipole moment. I
calculated autocorrelation function for each run and averaged over 50.

Regards,
Chathurika.

On Wed, Jun 29, 2011 at 10:39 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Tue, Jun 28, 2011 at 8:27 PM, Chathurika Abeyrathne
> <c.abeyrathne_at_student.unimelb.edu.au> wrote:
> > Dear Dr. Axel,
> >
> > Thank you for your time.
> >
> > I obtained the total dipole moment from VMD.
>
> how exactly?
>
> > Then I calculated autocorrelation function of total dipole moment as in
> Eq.
> > (5) (Please find the attached paper).
>
> this is the standard way how _any_ auto-correlation works
> and featured in almost any text book on MD. no need to
> send me a paper for that.
>
> > This autocorrelation function should decrease exponentially to zero (Fig.
> > 5).
>
> > However, when I calculated the autocorrelation function, it goes to
> negative
> > side too.
>
> yes, but the total dipole auto-correlation is a very difficult to
> converge property. it depends on the dielectric boundary conditions
> of your simulation and generally requires great care to get right.
>
> how long a trajectory, and what length of
> a time window did you compute/average it over?
>
> axel.
>
> p.s.: please always send a copy of your response to the vmd-l mailing
> list. this way people get to see the response and how your problem is
> getting resolved (or not).
>
>
> >
> > Regards,
> > Chathurika.
> >
> >
> > On Wed, Jun 29, 2011 at 12:48 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> >>
> >> On Tue, Jun 28, 2011 at 5:48 AM, Chathurika Abeyrathne
> >> <c.abeyrathne_at_student.unimelb.edu.au> wrote:
> >> >
> >> >
> >> > Hi,
> >> >
> >> > I need to calculate the auto-correlation function (ACF) of total
> dipole
> >> > moment of Methanol box.
> >>
> >>
> >> > I obtained the total dipole moment from VMD and calculated the ACF
> >> > manually.
> >> > However, this gives negative values.
> >>
> >> sorry, i don't understand. what gives negative values of what
> >> when you are doing exactly what?
> >>
> >> > In the selection tab i selected "all" the molecules. I didn't change
> the
> >> > scale or radius.
> >>
> >> what "scale" or "radius" are you talking about and how is
> >> this related to computing the dipole moment.
> >>
> >> > Do these things affect the total dipole moment.
> >>
> >> what, "scale" and "radius". there is no relation. dipole
> >> moment is about charges and positions.
> >>
> >> axel.
> >>
> >> > Thank you.
> >> >
> >> > Regards,
> >> > Chathurika.
> >> >
> >>
> >>
> >>
> >> --
> >> Dr. Axel Kohlmeyer
> >> akohlmey_at_gmail.com http://goo.gl/1wk0
> >>
> >> Institute for Computational Molecular Science
> >> Temple University, Philadelphia PA, USA.
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>