VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jun 28 2011 - 20:02:59 CDT

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.