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 Thu Aug 04 2011 - 11:30:04 PDT
