# AMBER Archive (2008)Subject: Re: AMBER: cross time correlation function

From: fatima.chami_at_durham.ac.uk
Date: Wed Apr 23 2008 - 12:00:43 CDT

Quoting "David A. Case" <case_at_scripps.edu>:

>
> On Wed, Apr 23, 2008, fatima.chami_at_durham.ac.uk wrote:
> >
> > is there a way to work out the cross time correlation function (TCF) using
> the
> > unit vector of each inter-atomic vector ...cause the TCF exceeds one.
> >
>
> In the "analyze timecorr" command, you can make vec1 different from vec2,
> and
> you will get cross-correlation functions. The examples section in the ptraj
> manual has an example of this.

>
> However, I'm guessing that I don't really understand what you want. These
> auto- or cross-corrrelation functions are averages of Legendre polynomials
> (of
> order 2 by default), and hence should never be greater than unity. I can't
> tell from your statement ("the TCF exceeds one") if this what you found and
> you don't like it, or if this is what you expect, and you are *not* seeing
> it

("the TCF exceeds one") is what I found and I don't like it

> in the ptraj output. In any event, you will need to give details about
> exactly what commands you tried if there is much hope of getting real help
> remotely.

------------------------------------- crosscorrel.ptraj-------------
trajin ./../stack8w_no_wat.mdcrd
vector v1 :1_at_C6 corr :1_at_C4 order 2
vector v2 :2_at_C6 corr :2_at_C4 order 2
analyse timecorr vec1 v1 vec2 v2 tstep 2 norm out v1_v2_C6C4.out
----------------------------------------------------------------------

TCF starts to exceed one at some point of it evolution: please look at the end
of the output file v1_v2_C6C4.out
-----------------------------v1_v2_C6C4.out--------------------------------
Cross-correlation functions, normal type

***** Correlation functions *****
Time <P2>
0.000 1.0000
2.000 0.9924
4.000 0.9877
6.000 0.9828
8.000 0.9784
10.000 0.9741
12.000 0.9698
14.000 0.9660
16.000 0.9614
18.000 0.9571
20.000 0.9529
22.000 0.9486
.
.
.....

8182.000 1.6828
8184.000 1.6767
8186.000 1.6663
8188.000 1.6498
8190.000 1.6324
8192.000 1.6136
8194.000 1.6009
8196.000 1.5784
8198.000 1.5537
8200.000 1.5373
8202.000 1.5172
8204.000 1.4865
8206.000 1.4699
8208.000 1.4523
8210.000 1.4234
8212.000 1.3889
8214.000 1.3475
8216.000 1.3046
8218.000 1.2543
8220.000 1.2384
8222.000 1.2106
8224.000 1.1938
8226.000 1.1669
8228.000 1.1494
8230.000 1.1601
8232.000 1.1477
8234.000 1.1514
8236.000 1.1578
8238.000 1.1631
8240.000 1.1310
8242.000 1.1147
8244.000 1.0845
8246.000 1.0636
8248.000 1.0264
8250.000 1.0142
8252.000 0.9975
8254.000 0.9427
8256.000 0.8835
8258.000 0.8601
8260.000 0.8828
8262.000 0.8881
8264.000 0.8870
8266.000 0.8836
8268.000 0.8844
8270.000 0.9448
8272.000 0.9370
8274.000 0.8825
8276.000 0.9212
8278.000 0.8698
8280.000 0.9037
8282.000 0.8862
8284.000 0.9271
8286.000 0.7292
8288.000 0.9382
-----------------------------------------------------------------------------

best wishes

> ...dac
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