## VMD-L Mailing List

**From:** Chathurika Abeyrathne (*c.abeyrathne_at_student.unimelb.edu.au*)

**Date:** Tue Jun 28 2011 - 20:08:17 CDT

**Next message:**Chathurika Abeyrathne: "Re: Total Dipole Moment"**Previous message:**Chathurika Abeyrathne: "Re: Total Dipole Moment"**In reply to:**Axel Kohlmeyer: "Re: Total Dipole Moment"**Next in thread:**Axel Kohlmeyer: "Re: Total Dipole Moment"**Reply:**Axel Kohlmeyer: "Re: Total Dipole Moment"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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.
*

*>
*

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