VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jun 28 2011 - 20:11:47 CDT

On Tue, Jun 28, 2011 at 9:08 PM, Chathurika Abeyrathne
<c.abeyrathne_at_student.unimelb.edu.au> wrote:
> 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.

ok. so you wrote out a file then, right?

> I run 50 times from the same input.

that is not a good idea. you want to have samples that
are as independent as possible.

if you always start from the same input and the same
start configuration, you'll have highly correlated data
and it will be as if you are just analyzing a couple of
trajectories instead of 50.

axel.

> 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.
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.