Thanks for your kind reply as well as Sorry for resending the mail !!
Still my problem related to the correlation function is not solved. So I am sending the mail again.
I have generated a trajectory file for a protein for 1 ns. I set the time step 4 fs and I saved the coordinate after 100 steps that is 400fs.
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.
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?
For my present system 'tstep=0.4' and 'tcorr=1000'. Am I wright? Is the defalt unit for 'tstep' and 'tcorr' is 'pico second'?
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).
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?
With best regards
Sindrila
From: David A Case <case.biomaps.rutgers.edu>
To: Sindrila Dutta banik <sindrila.duttabanik.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Friday, 5 August 2011 12:10 AM
Subject: Re: [AMBER] Problem related to the correlation function
On Thu, Aug 04, 2011, Sindrila Dutta banik wrote:
>
> I am computing a correlation function using the following script
>
> 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
>
> I have few enquiry such as
> (i) what the tstep mean?
> (ii) what does mean by tcorr?
Please see p. 130 of the AmberTools Users' Manual.
> (iii) For a vector as mentioned in the above script 'order 2' is
> correct?
There is no "correct" or "incorrect": it depends on what you are planning
to do with the resulting time correlation function.
> (iv) For the present calculation the value correlation
> function is very high. after a long time? is there any wrong in script
> file?
I see that you copied these inputs from the examples. Are you sure that
you understand what things like "@5" are doing? For most molecules, the
cross-correlation listed above would never decay very far, but I'm not sure
what you mean by "very high after a long time". If we knew what correlation
functions you really want (and what you plan to do with them), we might be
able to offer some pointers.
....dac
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Received on Sat Aug 06 2011 - 09:30:02 PDT
