On Wed, Aug 10, 2011 at 9:02 AM, Sindrila Dutta banik <
sindrila.duttabanik.yahoo.com> wrote:
> Thanks for your reply!!
>
> I am trying to write a program by which I can compute the correlation
> function from the coordinates as you suggested. However, few questions arise
> in my mind which are as follows:
>
> First I extracted the coordinates from the mdcrd file as a function of
> time. (A file that contains time, number of atom, coordinate (x,y,z) in five
> column).
>
> Now I want to compute the electrical dipole moment in different time of a
> particular water molecule. To do this I need two variables (a) length
> between the two atoms and (b) partial charge over the two atoms. I get the
> Length from the coordinate file. But how shall I get the partial charge over
> the atoms?
>
This is stored in the topology file. See the website
http://ambermd.org/formats.html for hints on how to interpret the prmtop
format. Note the units that the electric charge is in!
HTH,
Jason
>
> Please let me know.
>
> With best regards
> Sindrila
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Aug 10 2011 - 16:00:03 PDT
