VMD-L Mailing List

From: Chathurika Abeyrathne (c.abeyrathne_at_student.unimelb.edu.au)
Date: Tue Jun 28 2011 - 20:08:17 CDT

 I loaded psf, pdb and dcd files to VMD. Then I go to Extensions ->
Visualization -> Dipole Moment Watcher. In dipole monitoring tool I select
all the molecules to obtain the total dipole moment.

I run 50 times from the same input.

Regards,
Chathurika.

On Wed, Jun 29, 2011 at 11:02 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Tue, Jun 28, 2011 at 8:56 PM, Chathurika Abeyrathne
> <c.abeyrathne_at_student.unimelb.edu.au> wrote:
> >
> > I loaded psf, pdb and dcd files to VMD and then I selected all the
> > molecules to obtain the total dipole moment.
>
> sorry, but i still don't get what you did,
>
> > 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
>
> the same input? or did you continue from a restart?
>
> axel.
>
> > 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.
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>