On 7/19/15 10:55 AM, Nilesh Dhumal wrote:
Erik,
I want autocorrelation function without normalization.
Use the -nonormalize option.
-Justin
Exact value at t=0, t=1 is with normalization.
Nilesh
Hi Nilesh,
I’m not sure what you mean. Both Ac_finSys and Ac are 1 at t=0. What
normalisation do you expect?
Kind regards,
Erik
Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College
Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ
On 19 Jul 2015, at 04:07, Nilesh Dhumal <ndhu...@andrew.cmu.edu> wrote:
Hello,
I am calculating autocorrelation function without normalization using
g_hbond
g_hbond -f test.pdb -s 3.tpr -nonormalize -n hydrogen_1.ndx -ac
./test/hbac_3.xvg -num ./test/num_3.xvg
The output, hbac_3.xvg, don't have normalized auto correlation
function.
Here is initial part
@ title "Hydrogen Bond Autocorrelation"
@ xaxis label "Time (ps)"
@ yaxis label "C(t)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ 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 6.67572e-06 0.761129
0.05 0.961928 0.992146 3398 0.401535
0.1 0.959846 0.991717 3496 0.0419408
0.15 0.957734 0.991281 3599 0.0340092
0.2 0.956446 0.991015 3660 0.022918
Why is it not normalized ?
Thanks,
Nilesh
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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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