[gmx-users] what do negative eigenvalues imply?
/> Hello, />>/ />>/ I was wondering if anybody can explain why eigenvalues can be negative? />>/ I have found a suggestion on the internet that this is because the />>/ positive eigenvalues have accounted for more than 100% of the motion. />>/ Does this sound accurate? /> No You normally have six negative eigevalues due to the fact that overall translation and rotation are removed. You have in addition 4 that are very small, maybe you can investigate how many degrees of freedom you have (it says in the md.log file). This should be equal to the umber of non-negative ev. Thanks for the explanation David. I have selected only the heavy atoms in the alanine dipeptide for the previously posted analysis. Therefore I made a new temperature coupling group composed only of these atoms and ran grompp in order to get the desired value output: "Number of degrees of freedom in T-Coupling group Protein_NoH is 23.98" So 24-6 is 18 and I am positive up to 20. I suppose it is ok that there are more (small) positive values than 18. If I re-do the analysis instead using all 22 atoms (include the H's) then grompp indicates: "Number of degrees of freedom in T-Coupling group Protein is 53.96" And I am positive up to ev #41 (g_covar eigenval.xvg follows) so 54-6 is 48, but I only have 41 positive. Nevertheless, the ev 42-48 are very small positive. # This file was created Mon Oct 29 18:45:06 2007 # by the following command: # /hpf/data/pomes/cneale/exe/gromacs-3.3.1/exec/fftw-3.1.2/bin/g_covar -s ../adp.tpr -n ../adp.ndx -f ../adp_0-1.56us.xtc -ascii covar.dat -mwa # # /hpf/data/pomes/cneale/exe/gromacs-3.3.1/exec/fftw-3.1.2/bin/g_covar is part of G R O M A C S: # # Gnomes, ROck Monsters And Chili Sauce # @title "Eigenvalues of the covariance matrix" @xaxis label "Eigenvector index" @yaxis label "(u nm\S2\N)" @TYPE xy 1 0.23291 2 0.0810199 3 0.0579589 4 0.0430226 5 0.0156911 6 0.015543 7 0.0154095 8 0.0153563 9 0.0153322 10 0.0151271 11 0.0122578 12 0.00725067 13 0.00261468 14 0.00179256 15 0.00165951 16 0.00103279 17 0.000815341 18 0.000572039 19 0.000508098 20 0.000365606 21 0.000359221 22 0.000352105 23 0.00035001 24 0.000344526 25 0.000259272 26 0.000258307 27 0.000251824 28 0.000201794 29 0.000134211 30 0.0001308 31 0.00010905 32 0.000107029 33 8.21594e-05 34 7.64162e-05 35 6.1539e-05 36 4.31456e-05 37 3.68485e-05 38 2.35955e-05 39 2.11371e-05 40 1.34103e-05 41 6.81332e-06 42 -1.17905e-06 43 -4.04147e-06 44 -9.72161e-06 45 -1.3889e-05 46 -3.51393e-05 47 -4.49705e-05 48 -6.51993e-05 49 -6.75307e-05 50 -7.47012e-05 51 -8.77501e-05 52 -0.00010138 53 -0.000103669 54 -0.000105253 55 -0.000106886 56 -0.000110613 57 -0.000111074 58 -0.000134431 59 -0.000166161 60 -0.000180943 61 -0.000204832 62 -0.000298183 63 -0.000444828 64 -0.00052514 65 -0.000592853 66 -0.00213633 Thanks, Chris. / />>/ This system is the alanine dipeptide. I do not find such negative values />>/ when running g_covar on full proteins. />>/ />>/ The contents of eigenval.xvg are listed below. />>/ />>/ # This file was created Mon Oct 29 16:31:46 2007 />>/ # by the following command: />>/ # /hpf/data/pomes/cneale/exe/gromacs-3.3.1/exec/fftw-3.1.2/bin/g_covar />>/ -s ../adp.tpr -n ../adp.ndx -f ../adp_0-1.56us.xtc -ascii covar.dat -mwa />>/ # />>/ is part of G R O M A C S: />>/ # />>/ # Great Red Owns Many ACres of Sand />>/ # />>/ @title "Eigenvalues of the covariance matrix" />>/ @xaxis label "Eigenvector index" />>/ @yaxis label "(u nm\S2\N)" />>/ @TYPE xy />>/ 1 0.211327 />>/ 2 0.0736961 />>/ 3 0.0522046 />>/ 4 0.04409 />>/ 5 0.0104057 />>/ 6 0.00577603 />>/ 7 0.00198832 />>/ 8 0.00163465 />>/ 9 0.00128302 />>/10 0.000735383 />>/11 0.000649576 />>/12 0.000434795 />>/13 0.000376401 />>/14 0.000337852 />>/15 0.000191994 />>/17 8.87514e-05 />>/18 7.31975e-05 />>/19 5.31939e-05 />>/20 4.45637e-05 />>/21 -5.03112e-06 />>/22 -1.26812e-05 />>/23 -2.48763e-05 />/>24 -5.90268e-05 />>/25 -0.000114215 />>/26 -0.000227912 />>/27 -0.000355243 />>/28 -0.000513052 />>/29 -0.000631471 />>/30 -0.00178302/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before pos
Re: [gmx-users] what do negative eigenvalues imply?
Chris Neale wrote: Hello, I was wondering if anybody can explain why eigenvalues can be negative? I have found a suggestion on the internet that this is because the positive eigenvalues have accounted for more than 100% of the motion. Does this sound accurate? No You normally have six negative eigevalues due to the fact that overall translation and rotation are removed. You have in addition 4 that are very small, maybe you can investigate how many degrees of freedom you have (it says in the md.log file). This should be equal to the umber of non-negative ev. This system is the alanine dipeptide. I do not find such negative values when running g_covar on full proteins. The contents of eigenval.xvg are listed below. # This file was created Mon Oct 29 16:31:46 2007 # by the following command: # /hpf/data/pomes/cneale/exe/gromacs-3.3.1/exec/fftw-3.1.2/bin/g_covar -s ../adp.tpr -n ../adp.ndx -f ../adp_0-1.56us.xtc -ascii covar.dat -mwa # # /hpf/data/pomes/cneale/exe/gromacs-3.3.1/exec/fftw-3.1.2/bin/g_covar is part of G R O M A C S: # # Great Red Owns Many ACres of Sand # @title "Eigenvalues of the covariance matrix" @xaxis label "Eigenvector index" @yaxis label "(u nm\S2\N)" @TYPE xy 1 0.211327 2 0.0736961 3 0.0522046 4 0.04409 5 0.0104057 6 0.00577603 7 0.00198832 8 0.00163465 9 0.00128302 10 0.000735383 11 0.000649576 12 0.000434795 13 0.000376401 14 0.000337852 15 0.000191994 16 0.000131498 17 8.87514e-05 18 7.31975e-05 19 5.31939e-05 20 4.45637e-05 21 -5.03112e-06 22 -1.26812e-05 23 -2.48763e-05 24 -5.90268e-05 25 -0.000114215 26 -0.000227912 27 -0.000355243 28 -0.000513052 29 -0.000631471 30 -0.00178302 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, 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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] what do negative eigenvalues imply?
Hello, I was wondering if anybody can explain why eigenvalues can be negative? I have found a suggestion on the internet that this is because the positive eigenvalues have accounted for more than 100% of the motion. Does this sound accurate? This system is the alanine dipeptide. I do not find such negative values when running g_covar on full proteins. The contents of eigenval.xvg are listed below. # This file was created Mon Oct 29 16:31:46 2007 # by the following command: # /hpf/data/pomes/cneale/exe/gromacs-3.3.1/exec/fftw-3.1.2/bin/g_covar -s ../adp.tpr -n ../adp.ndx -f ../adp_0-1.56us.xtc -ascii covar.dat -mwa # # /hpf/data/pomes/cneale/exe/gromacs-3.3.1/exec/fftw-3.1.2/bin/g_covar is part of G R O M A C S: # # Great Red Owns Many ACres of Sand # @title "Eigenvalues of the covariance matrix" @xaxis label "Eigenvector index" @yaxis label "(u nm\S2\N)" @TYPE xy 1 0.211327 2 0.0736961 3 0.0522046 4 0.04409 5 0.0104057 6 0.00577603 7 0.00198832 8 0.00163465 9 0.00128302 10 0.000735383 11 0.000649576 12 0.000434795 13 0.000376401 14 0.000337852 15 0.000191994 16 0.000131498 17 8.87514e-05 18 7.31975e-05 19 5.31939e-05 20 4.45637e-05 21 -5.03112e-06 22 -1.26812e-05 23 -2.48763e-05 24 -5.90268e-05 25 -0.000114215 26 -0.000227912 27 -0.000355243 28 -0.000513052 29 -0.000631471 30 -0.00178302 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
