[gmx-users] g_analyze -ee
Dear Gromacs Specialists, I have one problem about g_analyze -ee, May I ask you to help me, Please? When I do this program as g_analyze -f .xvg -av -ee, it is as followed: Read 4 sets of 83001 points, dt = 6 std. dev. relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 1.811675e+00 1.585145e-02 5.502120e-05 0.416 0.334 SS2 1.476938e+00 5.370597e-02 1.864162e-04 0.011 -0.009 SS3 1.482869e+00 5.208019e-02 1.807730e-04 -0.010 -0.034 SS4 1.475204e+00 5.259068e-02 1.825449e-04 0.012 -0.089 Back Off! I just backed up average.xvg to ./#average.xvg.2# Set 1: err.est. 0.00042 a 0.402275 tau1 14.2321 tau2 255.692 Set 2: err.est. 0.002757 a 0.870111 tau1 592.695 tau2 1081.59 Warning: tau2 is longer than the length of the data (498000) the statistics might be bad invalid fit: e.e. 0.476411 a 0.999161 tau1 572.985 tau2 2.48396e+10 Will fix tau2 at the total time: 498000 Set 3: err.est. 0.00341541 a 0.998996 tau1 571.479 tau2 498000 Set 4: err.est. 0.00360836 a 0.984581 tau1 578.453 tau2 39087.7 Then, I studied this article: J. Chem. Phys. 116, 209 (2002) In it has been written There are restrictions on the range of the fitting parameters: a should be between 0 and 1 and tau1 and tau2 should be larger than 0. When the longest correlation time, tau2 , is longer than the averaging interval and (1-a) tau2 is not negligible compared to a tau1 , there is not enough statistics to estimate the error. I thought that my problem is related to frequency to write coordinates and the other outputs to output trajectory file, then I changed it from 200 to 2000 in md.mdp file, but when I did g_analyze, again I took warning as following: Read 4 sets of 8001 points, dt = 60 std. dev. relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 1.811686e+00 1.577702e-02 1.763924e-04 0.422 0.376 SS2 1.476945e+00 5.345846e-02 5.976838e-04 0.004 -0.014 SS3 1.482819e+00 5.253597e-02 5.873700e-04 0.002 -0.034 SS4 1.475254e+00 5.289252e-02 5.913564e-04 0.021 -0.084 Back Off! I just backed up average.xvg to ./#average.xvg.1# Back Off! I just backed up errorgyrate1.xvg to ./#errorgyrate1.xvg.1# Set 1: err.est. 0.000415045 a 0.741181 tau1 93.389 tau2 374.375 Set 2: err.est. 0.00283072 a 0.964747 tau1 629.293 tau2 1869.63 a fitted parameter is negative invalid fit: e.e. 0.0025708 a 1.01686 tau1 576.241 tau2 663.907 Will fix tau2 at the total time: 48 Set 3: err.est. 0.00469726 a 0.997164 tau1 558.935 tau2 48 Set 4: err.est. 0.00371208 a 0.969329 tau1 551.965 tau2 21102.3 I don't know that where is my mistake and what thing should I change for fix of this warning! Please help me. Best Regards Dina-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_analyze -ee
Dear Justin, Thank you very much from your response. OK, but is it important? Because these warnings are appeared some where, not for all of calculations. For example, these are appeared for gyrate.xvg and not for moment.xvg! Thank you again from your help and excuse me from my delay for thank from you. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, February 18, 2012 5:29 PM Subject: Re: [gmx-users] g_analyze -ee dina dusti wrote: Dear Gromacs Specialists, Sometimes, when I do g_analyze -f .xvg -av -ee error.xvg , I take following warning, and I don't know how to fix it. Set 1: err.est. 0.000596502 a 0.29217 tau1 24.8856 tau2 443.641 Warning: tau2 is longer than the length of the data (864000) the statistics might be bad invalid fit: e.e. 0.285911 a 0.995985 tau1 1434.16 tau2 1.41932e+09 Will fix tau2 at the total time: 864000 Set 2: err.est. 0.00859257 a 0.995692 tau1 1432.7 tau2 864000 Set 3: err.est. 0.00527967 a 0.588024 tau1 804.83 tau2 3603.55 a fitted parameter is negative invalid fit: e.e. 0.00421461 a 1.08722 tau1 1672.3 tau2 6955.25 Will fix tau2 at the total time: 864000 a fitted parameter is negative invalid fit: e.e. -nan a 1.00449 tau1 1455.53 tau2 864000 Will use a single exponential fit for set 4 Set 4: err.est. 0.00453113 a 1 tau1 1400.34 tau2 0 Please help me. Thanks in advance from your response. It likely means the data are poorly converged. Refer to the paper cited in g_analyze -h regarding the error calculation for details and a complete description of the error estimate method. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_analyze -ee
dina dusti wrote: Dear Justin, Thank you very much from your response. OK, but is it important? Because these warnings are appeared some where, not for all of calculations. For example, these are appeared for gyrate.xvg and not for moment.xvg! The warnings indicate that the error estimates are not reliable. It's all to do with the autocorrelation time. Some quantities converge faster than others. The appendix of the cited paper in g_analyze -h explains the entire derivation and what each term means. -Justin Thank you again from your help and excuse me from my delay for thank from you. Best Regards Dina *From:* Justin A. Lemkul jalem...@vt.edu *To:* dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Saturday, February 18, 2012 5:29 PM *Subject:* Re: [gmx-users] g_analyze -ee dina dusti wrote: Dear Gromacs Specialists, Sometimes, when I do g_analyze -f .xvg -av -ee error.xvg , I take following warning, and I don't know how to fix it. Set 1: err.est. 0.000596502 a 0.29217 tau1 24.8856 tau2 443.641 Warning: tau2 is longer than the length of the data (864000) the statistics might be bad invalid fit: e.e. 0.285911 a 0.995985 tau1 1434.16 tau2 1.41932e+09 Will fix tau2 at the total time: 864000 Set 2: err.est. 0.00859257 a 0.995692 tau1 1432.7 tau2 864000 Set 3: err.est. 0.00527967 a 0.588024 tau1 804.83 tau2 3603.55 a fitted parameter is negative invalid fit: e.e. 0.00421461 a 1.08722 tau1 1672.3 tau2 6955.25 Will fix tau2 at the total time: 864000 a fitted parameter is negative invalid fit: e.e. -nan a 1.00449 tau1 1455.53 tau2 864000 Will use a single exponential fit for set 4 Set 4: err.est. 0.00453113 a 1 tau1 1400.34 tau2 0 Please help me. Thanks in advance from your response. It likely means the data are poorly converged. Refer to the paper cited in g_analyze -h regarding the error calculation for details and a complete description of the error estimate method. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_analyze -ee
Dear Justin, Thank you very much from your response. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, February 20, 2012 11:07 PM Subject: Re: [gmx-users] g_analyze -ee dina dusti wrote: Dear Justin, Thank you very much from your response. OK, but is it important? Because these warnings are appeared some where, not for all of calculations. For example, these are appeared for gyrate.xvg and not for moment.xvg! The warnings indicate that the error estimates are not reliable. It's all to do with the autocorrelation time. Some quantities converge faster than others. The appendix of the cited paper in g_analyze -h explains the entire derivation and what each term means. -Justin Thank you again from your help and excuse me from my delay for thank from you. Best Regards Dina *From:* Justin A. Lemkul jalem...@vt.edu *To:* dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Saturday, February 18, 2012 5:29 PM *Subject:* Re: [gmx-users] g_analyze -ee dina dusti wrote: Dear Gromacs Specialists, Sometimes, when I do g_analyze -f .xvg -av -ee error.xvg , I take following warning, and I don't know how to fix it. Set 1: err.est. 0.000596502 a 0.29217 tau1 24.8856 tau2 443.641 Warning: tau2 is longer than the length of the data (864000) the statistics might be bad invalid fit: e.e. 0.285911 a 0.995985 tau1 1434.16 tau2 1.41932e+09 Will fix tau2 at the total time: 864000 Set 2: err.est. 0.00859257 a 0.995692 tau1 1432.7 tau2 864000 Set 3: err.est. 0.00527967 a 0.588024 tau1 804.83 tau2 3603.55 a fitted parameter is negative invalid fit: e.e. 0.00421461 a 1.08722 tau1 1672.3 tau2 6955.25 Will fix tau2 at the total time: 864000 a fitted parameter is negative invalid fit: e.e. -nan a 1.00449 tau1 1455.53 tau2 864000 Will use a single exponential fit for set 4 Set 4: err.est. 0.00453113 a 1 tau1 1400.34 tau2 0 Please help me. Thanks in advance from your response. It likely means the data are poorly converged. Refer to the paper cited in g_analyze -h regarding the error calculation for details and a complete description of the error estimate method. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_analyze -ee
Dear Gromacs Specialists, Sometimes, when I do g_analyze -f .xvg -av -ee error.xvg , I take following warning, and I don't know how to fix it. Set 1: err.est. 0.000596502 a 0.29217 tau1 24.8856 tau2 443.641 Warning: tau2 is longer than the length of the data (864000) the statistics might be bad invalid fit: e.e. 0.285911 a 0.995985 tau1 1434.16 tau2 1.41932e+09 Will fix tau2 at the total time: 864000 Set 2: err.est. 0.00859257 a 0.995692 tau1 1432.7 tau2 864000 Set 3: err.est. 0.00527967 a 0.588024 tau1 804.83 tau2 3603.55 a fitted parameter is negative invalid fit: e.e. 0.00421461 a 1.08722 tau1 1672.3 tau2 6955.25 Will fix tau2 at the total time: 864000 a fitted parameter is negative invalid fit: e.e. -nan a 1.00449 tau1 1455.53 tau2 864000 Will use a single exponential fit for set 4 Set 4: err.est. 0.00453113 a 1 tau1 1400.34 tau2 0 Please help me. Thanks in advance from your response. Best Regards Dina-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_analyze -ee
Dear all I used g_analyze -f dist.xvg -ee In the one of the my output files, I encountered Read 1 sets of 1252 points, dt = 0.0119951 std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 7.918456e+00 2.788148e+00 7.882919e-02 -0.717 -0.202 Back Off! I just backed up e11grey.xvg to ./#e11grey.xvg.2# Warning: tau2 is longer than the length of the data (15.0059) the statistics might be bad invalid fit: e.e. nan a 2.07331 tau1 3.99138 tau2 183052 Will fix tau2 at the total time: 15.0059 a fitted parameter is negative invalid fit: e.e. nan a 16.5523 tau1 10.8852 tau2 15.0059 Will use a single exponential fit for set 1 Set 1: err.est. 1.26673 a 1 tau1 1.54994 tau2 0 how to fix that? Best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_analyze -ee
Dear gromacs users I want to calculate error estimates using block averaging for output from g-dist (distance between donor atom of protein and acceptor atom of dna). I used g_analyze -f dist.xvg -ee there are 3 columns in output file. anyone give me more explain about these columns? how to explicate and interpret these data? In the one of the my output files, I encountered Read 1 sets of 1252 points, dt = 0.0119951 std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 7.918456e+00 2.788148e+00 7.882919e-02 -0.717 -0.202 Back Off! I just backed up e11grey.xvg to ./#e11grey.xvg.2# Warning: tau2 is longer than the length of the data (15.0059) the statistics might be bad invalid fit: e.e. nan a 2.07331 tau1 3.99138 tau2 183052 Will fix tau2 at the total time: 15.0059 a fitted parameter is negative invalid fit: e.e. nan a 16.5523 tau1 10.8852 tau2 15.0059 Will use a single exponential fit for set 1 Set 1: err.est. 1.26673 a 1 tau1 1.54994 tau2 0 how to fix that? Best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_analyze -ee
On 30/12/2011 1:06 AM, leila karami wrote: Dear gromacs users I want to calculate error estimates using block averaging for output from g-dist (distance between donor atom of protein and acceptor atom of dna). I used g_analyze -f dist.xvg -ee there are 3 columns in output file. anyone give me more explain about these columns? Have you read g_analyze -h and perhaps consulted the reference you can find there? Mark how to explicate and interpret these data? In the one of the my output files, I encountered Read 1 sets of 1252 points, dt = 0.0119951 std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 7.918456e+00 2.788148e+00 7.882919e-02 -0.717 -0.202 Back Off! I just backed up e11grey.xvg to ./#e11grey.xvg.2# Warning: tau2 is longer than the length of the data (15.0059) the statistics might be bad invalid fit: e.e. nan a 2.07331 tau1 3.99138 tau2 183052 Will fix tau2 at the total time: 15.0059 a fitted parameter is negative invalid fit: e.e. nan a 16.5523 tau1 10.8852 tau2 15.0059 Will use a single exponential fit for set 1 Set 1: err.est. 1.26673 a 1 tau1 1.54994 tau2 0 how to fix that? Best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
