Hi Tom,
Thanks for your response.
Indeed I did some digging and found similar answers to what you explained in your response.
It seems to me that the covariance method is not appropriate to the autocorrelation analysis of H-bonds. The physical interpretation of the autocorrelation function of H-bonds cannot allow negative numbers since they have no real meaning. It is not possible that the H-bonds as a function of time will be less than 0.
So I prefer the no-covariance method. And to the point of the negative values being small I am pasting the head and tail of the autocorrelation file (I don’t want to send a file of about 20Mb).
[osmanr01.minerva2 HBN_new]$ head mcmrjp_free_auc.dat
#Frame SER_252.OG-GLN_17.NE2-HE21 GLU_206.OE1-ARG_67.NH2-HH21 GLU_207.OE1-GLU_207.N-HN ASP_159.OD1-LEU_272.N-HN LEU_32.O-ALA_34.N-HN GLU_206.OE1-ARG_67.NE-HE GLU_207.OE2-GLU_207.N-HN MET_27.O-LEU_32.N-HN GLU_206.OE1-GLU_206.N-HN GLU_206.OE2-ARG_67.NH2-HH21 GLU_206.OE2-ARG_67.NE-HE ASN_267.OD1-ASN_267.N-HN GLU_206.OE2-GLU_206.N-HN SER_228.OG-THR_245.OG1-HG1 ASP_159.O-SER_162.OG-HG1 ILE_183.O-ARG_165.NH2-HH21 ILE_183.O-ARG_165.NH1-HH12 LEU_143.O-SER_39.OG-HG1 GLN_17.OE1-SER_252.OG-HG1 PHE_262.O-ASN_267.N-HN ILE_183.O-ARG_165.NH2-HH22 ASP_159.O-SER_162.N-HN ILE_183.O-ARG_165.NH1-HH11 PHE_262.O-ASN_267.ND2-HD22 LEU_143.O-SER_39.N-HN ILE_138.O-ALA_34.N-HN ALA_290.O-TRP_239.N-HN SER_39.OG-LEU_143.N-HN GLU_204.OE2-GLU_204.N-HN SER_228.O-THR_245.OG1-HG1 THR_245.OG1-SER_228.OG-HG1 SER_162.OG-ARG_165.NH2-HH22 ASN_267.N-ASN_267.ND2-HD22 SER_162.OG-ARG_165.NH2-HH21 SER_39.O-SER_39.OG-HG1 GLU_204.OE1-GLU_204.N-HN SER_162.OG-ARG_165.NH1-HH12 GLU_206.OE2-GLU_207.N-HN GLU_206.OE1-GLU_207.N-HN GLU_207.OE2-ARG_67.NH2-HH22 GLU_207.OE1-ARG_67.NH2-HH22 GLU_207.OE1-ARG_67.NH1-HH12 ASN_267.O-ASN_267.ND2-HD22 GLU_207.OE2-ARG_67.NH1-HH12 GLU_204.OE2-ARG_165.NH2-HH22 GLU_204.OE1-ARG_165.NH2-HH22 GLU_204.OE2-ARG_165.NE-HE GLU_204.OE1-ARG_165.NE-HE SER_162.OG-ARG_165.NE-HE GLU_204.OE1-SER_162.OG-HG1 GLU_204.OE2-SER_162.OG-HG1 THR_245.O-THR_245.OG1-HG1 SER_162.O-ARG_165.N-HN
1 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000
2 0.0721 0.6501 0.5482 0.0435 0.7039 0.6613 0.5578 0.2746 0.4896 0.6424 0.6097 0.0550 0.4984 0.3454 0.0332 0.6625 0.2496 0.4906 0.3219 0.1388 0.1665 0.0153 0.6523 0.1276 0.4999 0.2507 0.6944 0.5782 0.6742 0.1138 0.3937 0.1370 -0.0004 -0.0007 0.1365 0.6990 -0.0002 0.4305 0.4188 0.8062 0.7776 0.2849 0.3748 0.2639 0.8693 0.8817 0.9375 0.9175 -0.0001 0.9373 0.9177 -0.0000 -0.0001
3 0.0672 0.6179 0.4871 0.0233 0.6920 0.6346 0.4693 0.2685 0.5481 0.6145 0.5838 -0.0006 0.3383 0.3381 0.0683 0.6378 0.3121 0.4227 0.2500 0.1359 -0.0002 0.0153 0.6539 0.1406 0.3332 0.2649 0.6928 0.5731 0.6396 0.0753 0.3276 0.1017 0.0765 0.1047 0.1057 0.6287 -0.0002 0.3679 0.3446 0.7514 0.7132 0.2675 0.1248 0.2430 0.8561 0.8697 0.9312 0.9092 -0.0001 0.9284 0.9026 -0.0000 -0.0001
4 0.0581 0.6033 0.4435 0.0278 0.6826 0.6141 0.4133 0.2565 0.4310 0.5934 0.5630 -0.0006 0.3383 0.3354 0.0683 0.6214 0.1871 0.3141 0.2500 0.1263 -0.0002 -0.0020 0.6454 0.0885 0.3332 0.2493 0.6882 0.5710 0.6257 0.0367 0.3276 0.1458 -0.0004 -0.0007 0.1211 0.5886 -0.0002 0.3321 0.3198 0.7093 0.6641 0.2540 0.1248 0.2281 0.8470 0.8630 0.9253 0.9013 -0.0001 0.9185 0.8937 -0.0000 -0.0001
5 0.0548 0.5836 0.3982 0.0353 0.6802 0.5893 0.3628 0.2509 0.4812 0.5725 0.5473 -0.0006 0.3490 0.3240 0.0508 0.6296 0.1245 0.3412 0.2295 0.1204 0.1665 -0.0020 0.6437 0.0755 0.3332 0.2445 0.6860 0.5638 0.5980 0.0945 0.1953 0.1634 -0.0004 -0.0007 0.0903 0.5986 -0.0002 0.2903 0.2992 0.6788 0.6252 0.2463 0.2498 0.2042 0.8402 0.8558 0.9204 0.8979 -0.0001 0.9136 0.8836 -0.0000 -0.0001
6 0.0557 0.5651 0.3371 0.0299 0.6802 0.5709 0.3214 0.2504 0.4561 0.5609 0.5351 -0.0006 0.3169 0.3133 0.0332 0.5720 0.1871 0.3888 0.2346 0.1093 0.3332 -0.0020 0.6442 0.1015 0.3332 0.2391 0.6884 0.5602 0.5980 0.0560 0.1622 0.1017 -0.0004 -0.0007 0.0748 0.4983 -0.0002 0.2784 0.2841 0.6522 0.5990 0.2173 0.2498 0.2042 0.8342 0.8501 0.9157 0.8891 -0.0001 0.9096 0.8799 -0.0000 -0.0001
7 0.0504 0.5545 0.3022 0.0274 0.6842 0.5594 0.2871 0.2548 0.3389 0.5426 0.5142 -0.0006 0.2636 0.3184 0.0156 0.5802 0.2496 0.3412 0.2089 0.1148 -0.0002 0.0153 0.6448 0.0234 0.3332 0.2449 0.6889 0.5554 0.5911 0.0945 0.1622 0.1370 -0.0004 -0.0007 0.0286 0.4983 -0.0002 0.2665 0.2580 0.6232 0.5696 0.2443 0.1248 0.1997 0.8302 0.8479 0.9104 0.8847 -0.0001 0.9034 0.8731 -0.0000 -0.0001
8 0.0467 0.5422 0.2970 0.0214 0.6755 0.5464 0.2618 0.2553 0.4226 0.5289 0.5000 -0.0006 0.3063 0.3228 0.0683 0.5720 0.1871 0.3480 0.1833 0.1154 -0.0002 -0.0020 0.6424 0.0494 0.1665 0.2418 0.6875 0.5556 0.6049 0.0753 0.1402 0.1193 -0.0004 -0.0007 0.0440 0.4481 -0.0002 0.2381 0.2319 0.6053 0.5433 0.1921 -0.0003 0.1997 0.8251 0.8410 0.9059 0.8813 -0.0001 0.8996 0.8696 -0.0000 -0.0001
9 0.0577 0.5306 0.2814 0.0315 0.6882 0.5356 0.2240 0.2634 0.3975 0.5201 0.4939 -0.0006 0.3063 0.3105 0.0332 0.5802 0.1245 0.2869 0.2038 0.1033 -0.0002 0.0153 0.6370 0.0234 0.1665 0.2357 0.6858 0.5527 0.5980 0.0367 0.0850 0.1017 -0.0004 -0.0007 0.0286 0.4180 -0.0002 0.2337 0.2058 0.5850 0.5163 0.2153 -0.0003 0.1923 0.8206 0.8402 0.9046 0.8770 -0.0001 0.8969 0.8659 -0.0000 -0.0001
and here is the tail:
[osmanr01.minerva2 HBN_new]$ tail mcmrjp_free_auc.dat
14491 0.0005 -0.0063 -0.0085 -0.0059 -0.0239 -0.0221 -0.0063 -0.0296 -0.0021 0.0047 -0.0233 -0.0003 -0.0016 0.0047 -0.0010 -0.0021 -0.0003 -0.0026 0.0069 -0.0192 -0.0001 -0.0010 -0.1208 -0.0013 -0.0001 0.0006 -0.1704 -0.0677 -0.0025 -0.0009 -0.0016 -0.0020 -0.0002 -0.0003 -0.0011 -0.0017 -0.0001 -0.0047 -0.0120 -0.0340 -0.0369 0.0043 -0.0001 -0.0091 0.0683 -0.2507 -0.2187 0.0405 -0.0000 -0.2210 0.0144 -0.0000 -0.0000
14492 0.0105 -0.0033 -0.0103 0.0020 -0.0239 -0.0261 -0.0063 -0.0240 -0.0021 0.0033 -0.0221 -0.0003 -0.0016 0.0114 -0.0010 -0.0021 -0.0003 -0.0026 0.0120 -0.0111 -0.0001 -0.0010 -0.1194 -0.0013 -0.0001 -0.0009 -0.1704 -0.0671 -0.0025 -0.0009 -0.0016 -0.0020 -0.0002 -0.0003 -0.0011 -0.0017 -0.0001 -0.0091 -0.0120 -0.0330 -0.0341 0.0081 -0.0001 -0.0106 0.0678 -0.2506 -0.2187 0.0402 -0.0000 -0.2207 0.0151 -0.0000 -0.0000
14493 0.0044 -0.0035 -0.0103 -0.0004 -0.0240 -0.0232 -0.0099 -0.0324 -0.0021 0.0041 -0.0190 -0.0003 -0.0016 0.0025 -0.0010 -0.0021 -0.0003 -0.0026 0.0017 -0.0209 -0.0001 -0.0010 -0.1213 -0.0013 -0.0001 -0.0015 -0.1704 -0.0693 -0.0025 -0.0009 -0.0016 -0.0020 -0.0002 -0.0003 -0.0011 -0.0017 -0.0001 -0.0062 -0.0119 -0.0326 -0.0345 0.0043 -0.0001 -0.0106 0.0681 -0.2507 -0.2187 0.0403 -0.0000 -0.2207 0.0152 -0.0000 -0.0000
14494 0.0064 -0.0044 -0.0103 -0.0014 -0.0240 -0.0245 -0.0081 -0.0298 -0.0021 0.0051 -0.0189 -0.0003 -0.0016 0.0066 -0.0010 -0.0021 -0.0003 -0.0026 0.0069 -0.0169 -0.0001 -0.0010 -0.1216 -0.0013 -0.0001 -0.0042 -0.1704 -0.0676 -0.0025 -0.0009 -0.0016 -0.0020 -0.0002 -0.0003 -0.0011 -0.0017 -0.0001 -0.0121 -0.0133 -0.0317 -0.0349 0.0062 -0.0001 -0.0106 0.0676 -0.2511 -0.2185 0.0399 -0.0000 -0.2208 0.0148 -0.0000 -0.0000
14495 0.0036 -0.0036 -0.0103 -0.0025 -0.0240 -0.0250 -0.0081 -0.0338 -0.0021 0.0066 -0.0165 -0.0003 -0.0016 0.0115 -0.0010 -0.0021 -0.0003 -0.0026 0.0120 -0.0237 -0.0001 -0.0010 -0.1208 -0.0013 -0.0001 -0.0018 -0.1704 -0.0676 -0.0025 -0.0009 -0.0016 -0.0020 -0.0002 -0.0003 -0.0011 -0.0017 -0.0001 -0.0106 -0.0133 -0.0313 -0.0334 0.0043 -0.0001 -0.0091 0.0687 -0.2509 -0.2187 0.0398 -0.0000 -0.2209 0.0143 -0.0000 -0.0000
14496 0.0137 -0.0085 -0.0103 0.0069 -0.0240 -0.0233 -0.0081 -0.0238 -0.0021 0.0051 -0.0168 -0.0003 -0.0016 0.0069 -0.0010 -0.0021 -0.0003 -0.0026 0.0017 -0.0141 -0.0001 -0.0010 -0.1236 -0.0013 -0.0001 -0.0038 -0.1705 -0.0666 -0.0025 -0.0009 -0.0016 -0.0020 -0.0002 -0.0003 -0.0011 -0.0017 -0.0001 -0.0091 -0.0105 -0.0305 -0.0321 0.0023 -0.0001 -0.0061 0.0682 -0.2511 -0.2189 0.0399 -0.0000 -0.2209 0.0146 -0.0000 -0.0000
14497 0.0014 -0.0048 -0.0103 0.0012 -0.0240 -0.0227 -0.0045 -0.0266 -0.0021 0.0057 -0.0133 -0.0003 -0.0016 0.0068 -0.0010 -0.0021 -0.0003 -0.0026 0.0120 -0.0221 -0.0001 -0.0010 -0.1191 -0.0013 -0.0001 -0.0031 -0.1705 -0.0685 -0.0025 -0.0009 -0.0016 -0.0020 -0.0002 -0.0003 -0.0011 -0.0017 -0.0001 -0.0106 -0.0118 -0.0315 -0.0306 0.0023 -0.0001 -0.0076 0.0677 -0.2506 -0.2187 0.0397 -0.0000 -0.2211 0.0147 -0.0000 -0.0000
14498 0.0037 -0.0071 -0.0103 -0.0001 -0.0240 -0.0218 -0.0009 -0.0275 -0.0021 0.0053 -0.0165 -0.0003 -0.0016 0.0146 -0.0010 -0.0021 -0.0003 -0.0026 0.0120 -0.0178 -0.0001 0.0163 -0.1217 -0.0013 -0.0001 -0.0007 -0.1705 -0.0656 -0.0025 -0.0009 -0.0016 -0.0020 -0.0002 -0.0003 -0.0011 -0.0017 -0.0001 -0.0091 -0.0118 -0.0311 -0.0301 -0.0015 -0.0001 -0.0106 0.0674 -0.2505 -0.2188 0.0396 -0.0000 -0.2212 0.0145 -0.0000 -0.0000
14499 0.0029 -0.0063 -0.0085 -0.0001 -0.0240 -0.0211 0.0027 -0.0258 -0.0021 0.0047 -0.0189 -0.0003 -0.0016 0.0087 -0.0010 -0.0021 -0.0003 -0.0026 0.0069 -0.0241 -0.0001 -0.0010 -0.1206 -0.0013 -0.0001 -0.0009 -0.1705 -0.0658 -0.0025 -0.0009 -0.0016 -0.0020 -0.0002 -0.0003 -0.0011 -0.0017 -0.0001 -0.0077 -0.0118 -0.0300 -0.0294 0.0023 -0.0001 -0.0106 0.0678 -0.2505 -0.2188 0.0395 -0.0000 -0.2212 0.0142 -0.0000 -0.0000
14500 0.0098 -0.0049 -0.0103 -0.0059 -0.0240 -0.0230 0.0009 -0.0346 -0.0021 0.0022 -0.0149 -0.0003 -0.0016 0.0082 -0.0010 -0.0021 -0.0003 -0.0026 0.0069 -0.0204 -0.0001 -0.0010 -0.1202 -0.0013 -0.0001 -0.0012 -0.1705 -0.0707 -0.0025 -0.0009 -0.0016 -0.0020 -0.0002 -0.0003 -0.0011 -0.0017 -0.0001 -0.0062 -0.0118 -0.0287 -0.0282 0.0062 -0.0001 -0.0076 0.0679 -0.2498 -0.2188 0.0398 -0.0000 -0.2213 0.0138 -0.0000 -0.0000
As you can see some values are -0.2(!) or worse.
This disappears when I use nocovar.
Anyway, what I think you imply is that the calculations are OK. I and my colleague coded the calculation of the autocorrelation of the H-bonds but we obtain different results from the autocorr in amber. Is there a test case where the results have been corroborated. We could see if the problem is in our code or in the data.
Thanks for your help,
Rami
On Aug 30, 2016, at 6:07 PM, Tom Kurtzman <simpleliquid.gmail.com<mailto:simpleliquid.gmail.com>> wrote:
Hi Roman, in response to your comment "In my opinion this is not possible
since the track is made of 0 and 1, so the autocorrelation cannot be < 0."
Often correlation functions (including autocorrelation functions) are
normalized so that their initial values are 1 and absence of correlation is
zero so instead of calculating
<A(t)A(t')> they actually calculate This is the same as calculating
<[A(t) -<A>][A(t')-<A>]> = <A(t)A(t')> - <A>^2. This allows for negative
numbers and ensures that the limit as t --> \infty is zero. Often the
function is then divided by its initial value to give an initial value
(upper bound) value of unity.
For the no-covariance calculation, I assume that the average values are not
subtracted and hence the limit and infinite time approaches <A>^2 which is
positive.
It is not unusual for autocorrelation functions to have negative values nor
to have long time non-zero tails (the velocity autocorrelation function is
a famous example of both of these) however, I'm not sure whether the long
time tail you are seeing is
1) real
2) fluctuations about zero due to sampling limitations (noise)
3) an artifact of an incorrectly calculated quantity.
Without seeing the data, I would initially suspect it's just noise.
Tom
On Mon, Aug 29, 2016 at 9:05 AM, Osman, Roman <roman.osman.mssm.edu<mailto:roman.osman.mssm.edu>> wrote:
Hello Amberites,
I was wondering whether anybody has used an autocorrelation of hydrogen
bonds.
Here is a cpptraj input that I ran:
# Read in trajectory
trajin mcmrjp_free_nw.dcd
hbond HB out mcmrjp_free_hb.dat :17,252,67,206,159,272,27,32,
228,245,262,267,165
,183,34,138,239,290,39,143,207,204,162 series uuseries mcmrjp_free_hb.dat
avgout
mcmrjp_free_avg.dat printatomnum
run
runanalysis lifetime HB[solutehb] out mcmrjp_free_lifet.dat
autocorr HB[solutehb] out mcmrjp_free_auc.dat lagmax 14500
run
The surprising thing is that I get in the aucorrelation function negative
numbers towards the end of the track.
In my opinion this is not possible since the track is made of 0 and 1, so
the autocorrelation cannot be < 0.
In fact if I run with
autocorr HB[solutehb] out mcmrjp_free_auc.dat lagmax 14500 nocovar
The autocorrelations become positive.
Am I doing something wrong?
Thanks for your help.
PS: I can provide the trajectory (large) and the output from the
autocorrelation.
Roman Osman
Professor of Structural and Chemical Biology
Mount Sinai School of Medicine
New York, NY 10029
(212) 659-8627
roman.osman.mssm.edu<mailto:roman.osman.mssm.edu><mailto:
roman.osman.mssm.edu>
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Department of Chemistry
Lehman College, CUNY
250 Bedford Park Blvd. West
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Roman Osman
Professor of Structural and Chemical Biology
Mount Sinai School of Medicine
New York, NY 10029
(212) 659-8627
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roman.osman.mssm.edu>
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Received on Tue Aug 30 2016 - 15:00:02 PDT
