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?
Please let me know.
With best regardsSindrila
----- Original Message -----
From: David A Case <case.biomaps.rutgers.edu>
To: Sindrila Dutta banik <sindrila.duttabanik.yahoo.com>
Cc:
Sent: Tuesday, 9 August 2011 1:31 AM
Subject: Re: [AMBER] Problem related to the correlation function
On Tue, Aug 09, 2011, Sindrila Dutta banik wrote:
>
> But I want to point out one thing. I go through a paper by M. Karplus
> and G.R. Fleming Ref: "Biochemistry, year 1988, Volume 27, page
> 6908" where the correlation fuunction for the atomic fluctuation have
> calculated.
Correlation functions like those of Eq. 4 in the above paper are not
handled by Amber analysis codes; (they are not very directly related
to experiment). Those like Eq. 11 are the "order 2" time correlation
functions that ptraj *can* compute.
However, you can compute your own time correlation functions for any parameter
that can be dumped as a function of time. So: you get something like Eq.4
by computing the average structure (after RMS fitting), then extracting the
coordinates vs. time (say by a strip command, may something else is easier),
then computing delta(r)(t), then autocorrelating the result. Once you do
this, you will have the advantage of understanding in detail what is going on.
>
> First I want to compute electrical dipole autocorrelation function for
> the water molecules
I don't think this is directly available in ptraj, although it is likely that
the O--H vector would be a good surrogate for this.
> by the electrical dipole autocorrelation function for the N-H bond of
> protein
Are you sure this is what you want? Are you using the N-H bond as a surrogate
for a transition dipole moment? If you can write it mathematically as in Eq.
11, then ptraj will make it easy.
> as well as autocorrelation function for different structural
> parameters (such as bond length, bond angle, dihedral angle etc).
See above: you just need to dump the required parameters as a function of
time, then use a standard analysis/graphing package (I use xmgrace, but
there are lots of possibilities) to get the autocorrelations. Or, write
your own little script to do this.
Maybe others on the list will have good suggestions here.
....good luck...dac
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Received on Wed Aug 10 2011 - 06:00:06 PDT
