thanks for your kind reply.
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. Am I doing some mistake in understanding this? Please let me know. It will be very helpful for me.
Again I repeat that I have generate a trajectory file for a Protein for 1ns in explicit solvent model (TIP3P).
First I want to compute electrical dipole autocorrelation function for the water molecules which is well known (for bench marking). Followed by the electrical dipole autocorrelation function for the N-H bond of protein as well as autocorrelation function for different structural parameters (such as bond length, bond angle, dihedral angle etc).
Now I want to know how to do this using ptraj of AMBER? How shall I define the above mentioned vectors (electrical dipole moment vector or bond length vector or angle vector or dihedral angle vector) in the script file?
With best regards
Sindrila
From: case <case.biomaps.rutgers.edu>
To: Sindrila Dutta banik <sindrila.duttabanik.yahoo.com>
Sent: Sunday, 7 August 2011 1:36 AM
Subject: Re: [AMBER] Problem related to the correlation function
On Sat, Aug 06, 2011, Sindrila Dutta banik wrote:
>
>
> Now, I want to compute the correlation function for the 'atomic
> fluctuation' for few residues (such as η N atom of Arg259) as well as
> the dipole-dipole correlation function for 'N-H' bond.Â
Atomic fluctuations are mean square distances from an average position; they
are not related to time correlation functions. See the "atomfluct" command in
ptraj.
>
> So, what shall I write in the vector section for the two cases? I
> tried to do 'matrix'-'analyze matrix'-'analyze mode' for computing the
> dipole-dipole correlation function as mentioned in user manual. But I
> failed which I have already mentioned in a previous mail. Shall I
> repost the mail?
The "analyze matrix" and "analyze mode" commands are not relevant.
>
> Is the defalt unit for 'tstep' and 'tcorr' is 'pico second'?
Yes. Note that generally tcorr should be much shorter than the total length
of the trajectory.
>
> Can I give more than one input file (trajin) at a time for computing the
> correlation function for a particular system. Because I have 10 mdcrd
> files for 1ns (each for 100ps).
Yes.
>
> It is not clear to me that what is meant by .5 and .6 in the vector
> section as described in the manual. I think it referrs atom number
> 5. Is it wright? Â
Yes.
> > trajin MD.mdcrd
> > vector v0 .5 corr .6 order 2
> > vector v1 .7 corr .8 order 2
> > analyze timecorr vec1 v0 vec2 v1 tstep 1.0 tcorr 100.0 out v0.out
To calculate the (magnetic) dipole autocorrelation function between atoms 5
and 6 you would slightly modify the above:
> > trajin MD.mdcrd
> > vector v0 .5 corr .6 order 2
> > analyze timecorr vec1 v0 vec2 v0 tstep 1.0 tcorr 100.0 out v0.out
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Received on Mon Aug 08 2011 - 12:00:03 PDT
