On 2/22/10 9:47 AM, [email protected] wrote:
Hi
I used g_hbond for analyzing hydrogen bonds.
What is difference between [s0 legend "Ac\sfin sys\v{}\z{}(t)"] and [s1
legend "Ac(t)"] in hbac.xvg file in below?
First one is "corrected" for the fact that in a finite system the ACF
does not go to zero, since HBs will reform after a long time. There is a
better way to do this, by following the PBC of each molecule (as in mean
square deviation). This will be implemented in the next version.
@ title "Hydrogen Bond Autocorrelation"
@ xaxis label "Time (ps)"
@ yaxis label "C(t)"
@ s0 legend "Ac\sfin sys\v{}\z{}(t)"
@ s1 legend "Ac(t)"
@ s2 legend "Cc\scontact,hb\v{}\z{}(t)"
@ s3 legend "-dAc\sfs\v{}\z{}/dt"
0 1 1 -0.00217462 0.275102
2 0.4543 0.847763 0.0871663 0.144609
4 0.421563 0.83863 0.0883458 0.0141166
6 0.397833 0.83201 0.0893797 0.0101501
8 0.380963 0.827303 0.0896131 0.00766257
10 0.367183 0.823459 0.0899727 0.00601236
12 0.356914 0.820594 0.0902401 0.00526451
14 0.346125 0.817584 0.0900176 0.004734
Are both of them Are both of them Autocorrelation function?
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[email protected] [email protected] http://folding.bmc.uu.se
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