Re: [gmx-users] Problems with Jacobi diagonalization
Hi Dayle, Quite a number of posts here :) Okay, so there may indeed (still) be a mismatch. Maybe good noting that g_covar will also accept a .pdb file as reference. One way to be sure that things go right is to convert the .tpr to .pdb using the index with the group 'TDR': editconf -f topol.tpr -o TDR.pdb -n index.ndx Then use that file to convert the trajectory to .pdb: trjconv -s TDR.pdb -f traj.xtc -o traj.pdb You should be fine taking the system as the atoms should match now. To check if they do, visualize both topol.pdb and traj.pdb. You'll notice a mismatch by garbled atom types/names. You have to explicitly check for that. Such mismatches are a bit hard to spot, as the .xtc file does not contain atom metadata. Aside of that there is another possible cause for this error to occur, and that is when the system is split over the periodic boundaries. That will also break the routine, but will also immediately show up when visualizing the system as mentioned above. Then, by means of 'by the way', are you sure you want to use the -ref flag with g_covar? This means that the deviations are taken with respect to the reference coordinates rather than with respect to the average coordinates. This comes down to calculating a non-central second moment. To illustrate that, imagine tossing a dice to investigate the distribution of numbers. Fine, you come to an average and get the standard deviation the usual way. But what you do here is calculating the deviation from, say 5, rather than the average of 3.5, or worse even, from 8. Nice exercise to calculate the second moment you get in that case and to try and think of what it means. I don't say it has no meaning; in some cases it makes sense, but you'll have to have good reasons for doing it and justify the approach when it comes to publication. More so, it usually requires more thinking of what such results signify. Cheers, Tsjerk 2009/4/2 Dayle Smith daylemariesm...@gmail.com: Thanks, Mark- I re-ran a short MD simulation with TDR as the only xtc group, and used tpbconv to create a .tpr file with only TDR (tpxout.tpr) and ran g_covar with an index.ndx that contains only TPR (just to be safe!), g_covar -f traj.xtc -s tpxout.tpr -ref -n index.ndx and I still get the Jacobi error: Choose a group for the least squares fit Group 0 ( TDR) has 29 elements There is one group in the index Choose a group for the covariance analysis Group 0 ( TDR) has 29 elements There is one group in the index Calculating the average structure ... Reading frame 0 time 0.000 --- Program g_covar, VERSION 3.3.3 Source code file: nrjac.c, line: 129 Fatal error: Error: Too many iterations in routine JACOBI ~Dayle On Wed, Apr 1, 2009 at 6:22 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Justin A. Lemkul wrote: Dayle Smith wrote: Thanks for your help, Justin. I ran gmxcheck -c topol.tpr (12284 atoms in file) and gmxcheck -f traj.xtc (# Atoms 29). The difference is Indeed, that's the problem, then! the SOL atoms. I made another .tpr file with xtcgroups = TDR SOL, and now gmxcheck shows that the number of atoms in topol.tpr is 12284, but I still can't get g_covar to work. Maybe these are unrelated problems, I'm not sure. You haven't really changed anything. The xtc-grps parameter defines what was saved in the simulation. Setting it after the fact does not affect the already-produced .xtc file. What you need is a .tpr file that contains only TDR, so you would have to make modifications to your .top in order to generate this TDR-only .tpr file. Or use tpbconv - this is the other application for that utility. Mark ___ gmx-users mailing list gmx-us...@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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing list gmx-us...@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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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
Re: [gmx-users] Problems with Jacobi diagonalization
Hi there Tsjerk- There are a lot of helpful people on this list! I transferred my gromacs files to a different TeraGrid computer that runs gromacs-4.0.2, and now g_covar and the other diagonalizing routines work! I don't know what was wrong with gromacs-3.3.3 on that first computer, since I tried everyone's suggestions, and I sent a note to the system administrator. Thank you so much, Dayle PS: Thanks A LOT for mentioning the pitfalls of using -ref with g_covar!!! That was a close one. On Thu, Apr 2, 2009 at 12:25 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Dayle, Quite a number of posts here :) Okay, so there may indeed (still) be a mismatch. Maybe good noting that g_covar will also accept a .pdb file as reference. One way to be sure that things go right is to convert the .tpr to .pdb using the index with the group 'TDR': editconf -f topol.tpr -o TDR.pdb -n index.ndx Then use that file to convert the trajectory to .pdb: trjconv -s TDR.pdb -f traj.xtc -o traj.pdb You should be fine taking the system as the atoms should match now. To check if they do, visualize both topol.pdb and traj.pdb. You'll notice a mismatch by garbled atom types/names. You have to explicitly check for that. Such mismatches are a bit hard to spot, as the .xtc file does not contain atom metadata. Aside of that there is another possible cause for this error to occur, and that is when the system is split over the periodic boundaries. That will also break the routine, but will also immediately show up when visualizing the system as mentioned above. Then, by means of 'by the way', are you sure you want to use the -ref flag with g_covar? This means that the deviations are taken with respect to the reference coordinates rather than with respect to the average coordinates. This comes down to calculating a non-central second moment. To illustrate that, imagine tossing a dice to investigate the distribution of numbers. Fine, you come to an average and get the standard deviation the usual way. But what you do here is calculating the deviation from, say 5, rather than the average of 3.5, or worse even, from 8. Nice exercise to calculate the second moment you get in that case and to try and think of what it means. I don't say it has no meaning; in some cases it makes sense, but you'll have to have good reasons for doing it and justify the approach when it comes to publication. More so, it usually requires more thinking of what such results signify. Cheers, Tsjerk 2009/4/2 Dayle Smith daylemariesm...@gmail.com: Thanks, Mark- I re-ran a short MD simulation with TDR as the only xtc group, and used tpbconv to create a .tpr file with only TDR (tpxout.tpr) and ran g_covar with an index.ndx that contains only TPR (just to be safe!), g_covar -f traj.xtc -s tpxout.tpr -ref -n index.ndx and I still get the Jacobi error: Choose a group for the least squares fit Group 0 ( TDR) has29 elements There is one group in the index Choose a group for the covariance analysis Group 0 ( TDR) has29 elements There is one group in the index Calculating the average structure ... Reading frame 0 time0.000 --- Program g_covar, VERSION 3.3.3 Source code file: nrjac.c, line: 129 Fatal error: Error: Too many iterations in routine JACOBI ~Dayle On Wed, Apr 1, 2009 at 6:22 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Justin A. Lemkul wrote: Dayle Smith wrote: Thanks for your help, Justin. I ran gmxcheck -c topol.tpr (12284 atoms in file) and gmxcheck -f traj.xtc (# Atoms 29). The difference is Indeed, that's the problem, then! the SOL atoms. I made another .tpr file with xtcgroups = TDR SOL, and now gmxcheck shows that the number of atoms in topol.tpr is 12284, but I still can't get g_covar to work. Maybe these are unrelated problems, I'm not sure. You haven't really changed anything. The xtc-grps parameter defines what was saved in the simulation. Setting it after the fact does not affect the already-produced .xtc file. What you need is a .tpr file that contains only TDR, so you would have to make modifications to your .top in order to generate this TDR-only .tpr file. Or use tpbconv - this is the other application for that utility. Mark ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users
Re: [gmx-users] Problems with Jacobi diagonalization
Hi Dayle, Errm, really, the only cases I know of this error to occur is when I had a mismatch between the reference and trajectory. Did you specify xtc-groups? Did you shuffle the system? How did you assert that you have matching series? Have you tried using the reference and the trajectory to convert (part of) the trajectory to .pdb and visualize? If all else fails, can you send (a link to) an archive containing a single frame from the trajectory and the reference? Cheers, Tsjerk 2009/4/1 Dayle Smith daylemariesm...@gmail.com: Greetings--- I'm working with a DNA system, and all of the routines I've worked with that require Jacobi diagonalization (g_covar, g_rms, etc) fail with the Too many iterations in routine JACOBI error. I'm using gromacs-3.3.3 with ffamber99 on the NCSA Mercury cluster. I've searched the archives, and I've found several entries in which users are advised to check that the coordinates in the trajectory and structure files match (mine do). I've also tried running covariance analysis on a small ligand molecule, and I get the same error. I can get g_covar to work with -nofit, but then I can't run g_anaeig. I'm eagerly looking forward to your suggestions! Have a great day, Dayle Smith Department of Physics Whitman College ___ gmx-users mailing list gmx-us...@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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problems with Jacobi diagonalization
Hi Tsjerk, Thank you for your quick and helpful response. I defined xtc_grps = TDR in my .mdp file (then I use grompp -f mdpme.mdp -c confout.gro -p topol.top -o topol.tpr -np 8 -n index.ndx, index contains TDR and SOL) and run it with -np 8. I'm afraid that I don't understand what shuffling or matching series refers to (a clue that I'm doing something wrong). This g_covar error message is probably another clue: WARNING: number of atoms in tpx (29) and trajectory (29) do not match --- Program g_covar, VERSION 3.3.3 Source code file: nrjac.c, line: 129 Fatal error: Error: Too many iterations in routine JACOBI So the # of atoms is the same, but some other key ingredient doesn't match. Can you please enlighten me?! Thanks a lot, Dayle On Wed, Apr 1, 2009 at 11:12 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Dayle, Errm, really, the only cases I know of this error to occur is when I had a mismatch between the reference and trajectory. Did you specify xtc-groups? Did you shuffle the system? How did you assert that you have matching series? Have you tried using the reference and the trajectory to convert (part of) the trajectory to .pdb and visualize? If all else fails, can you send (a link to) an archive containing a single frame from the trajectory and the reference? Cheers, Tsjerk 2009/4/1 Dayle Smith daylemariesm...@gmail.com: Greetings--- I'm working with a DNA system, and all of the routines I've worked with that require Jacobi diagonalization (g_covar, g_rms, etc) fail with the Too many iterations in routine JACOBI error. I'm using gromacs-3.3.3 with ffamber99 on the NCSA Mercury cluster. I've searched the archives, and I've found several entries in which users are advised to check that the coordinates in the trajectory and structure files match (mine do). I've also tried running covariance analysis on a small ligand molecule, and I get the same error. I can get g_covar to work with -nofit, but then I can't run g_anaeig. I'm eagerly looking forward to your suggestions! Have a great day, Dayle Smith Department of Physics Whitman College ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problems with Jacobi diagonalization
Dayle Smith wrote: Hi Tsjerk, Thank you for your quick and helpful response. I defined xtc_grps = TDR in my .mdp file (then I use grompp -f mdpme.mdp -c confout.gro -p topol.top -o topol.tpr -np 8 -n index.ndx, index contains TDR and SOL) and run it with -np 8. I'm afraid that I don't understand what shuffling or matching series refers to (a clue that I'm doing something wrong). This g_covar error message is probably another clue: WARNING: number of atoms in tpx (29) and trajectory (29) do not match --- Program g_covar, VERSION 3.3.3 Source code file: nrjac.c, line: 129 Fatal error: Error: Too many iterations in routine JACOBI So the # of atoms is the same, but some other key ingredient doesn't match. Can you please enlighten me?! I think the output error message is bizarre, but you still have a number of atoms in the .tpr that does not match the .xtc. If your simulation is of TDR and SOL, then those groups will be in your topol.tpr. If your xtc-grps specify only TDR, then there will be a coordinate mismatch. Run the following: gmxcheck -c topol.tpr gmxcheck -f traj.xtc and see if gmxcheck reports the same number of atoms in both files. This is the quickest way to know for sure. -Justin Thanks a lot, Dayle On Wed, Apr 1, 2009 at 11:12 AM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hi Dayle, Errm, really, the only cases I know of this error to occur is when I had a mismatch between the reference and trajectory. Did you specify xtc-groups? Did you shuffle the system? How did you assert that you have matching series? Have you tried using the reference and the trajectory to convert (part of) the trajectory to .pdb and visualize? If all else fails, can you send (a link to) an archive containing a single frame from the trajectory and the reference? Cheers, Tsjerk 2009/4/1 Dayle Smith daylemariesm...@gmail.com mailto:daylemariesm...@gmail.com: Greetings--- I'm working with a DNA system, and all of the routines I've worked with that require Jacobi diagonalization (g_covar, g_rms, etc) fail with the Too many iterations in routine JACOBI error. I'm using gromacs-3.3.3 with ffamber99 on the NCSA Mercury cluster. I've searched the archives, and I've found several entries in which users are advised to check that the coordinates in the trajectory and structure files match (mine do). I've also tried running covariance analysis on a small ligand molecule, and I get the same error. I can get g_covar to work with -nofit, but then I can't run g_anaeig. I'm eagerly looking forward to your suggestions! Have a great day, Dayle Smith Department of Physics Whitman College ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
Re: [gmx-users] Problems with Jacobi diagonalization
Thanks for your help, Justin. I ran gmxcheck -c topol.tpr (12284 atoms in file) and gmxcheck -f traj.xtc (# Atoms 29). The difference is the SOL atoms. I made another .tpr file with xtcgroups = TDR SOL, and now gmxcheck shows that the number of atoms in topol.tpr is 12284, but I still can't get g_covar to work. Maybe these are unrelated problems, I'm not sure. ~Dayle On Wed, Apr 1, 2009 at 2:49 PM, Justin A. Lemkul jalem...@vt.edu wrote: Dayle Smith wrote: Hi Tsjerk, Thank you for your quick and helpful response. I defined xtc_grps = TDR in my .mdp file (then I use grompp -f mdpme.mdp -c confout.gro -p topol.top -o topol.tpr -np 8 -n index.ndx, index contains TDR and SOL) and run it with -np 8. I'm afraid that I don't understand what shuffling or matching series refers to (a clue that I'm doing something wrong). This g_covar error message is probably another clue: WARNING: number of atoms in tpx (29) and trajectory (29) do not match --- Program g_covar, VERSION 3.3.3 Source code file: nrjac.c, line: 129 Fatal error: Error: Too many iterations in routine JACOBI So the # of atoms is the same, but some other key ingredient doesn't match. Can you please enlighten me?! I think the output error message is bizarre, but you still have a number of atoms in the .tpr that does not match the .xtc. If your simulation is of TDR and SOL, then those groups will be in your topol.tpr. If your xtc-grps specify only TDR, then there will be a coordinate mismatch. Run the following: gmxcheck -c topol.tpr gmxcheck -f traj.xtc and see if gmxcheck reports the same number of atoms in both files. This is the quickest way to know for sure. -Justin Thanks a lot, Dayle On Wed, Apr 1, 2009 at 11:12 AM, Tsjerk Wassenaar tsje...@gmail.commailto: tsje...@gmail.com wrote: Hi Dayle, Errm, really, the only cases I know of this error to occur is when I had a mismatch between the reference and trajectory. Did you specify xtc-groups? Did you shuffle the system? How did you assert that you have matching series? Have you tried using the reference and the trajectory to convert (part of) the trajectory to .pdb and visualize? If all else fails, can you send (a link to) an archive containing a single frame from the trajectory and the reference? Cheers, Tsjerk 2009/4/1 Dayle Smith daylemariesm...@gmail.com mailto:daylemariesm...@gmail.com: Greetings--- I'm working with a DNA system, and all of the routines I've worked with that require Jacobi diagonalization (g_covar, g_rms, etc) fail with the Too many iterations in routine JACOBI error. I'm using gromacs-3.3.3 with ffamber99 on the NCSA Mercury cluster. I've searched the archives, and I've found several entries in which users are advised to check that the coordinates in the trajectory and structure files match (mine do). I've also tried running covariance analysis on a small ligand molecule, and I get the same error. I can get g_covar to work with -nofit, but then I can't run g_anaeig. I'm eagerly looking forward to your suggestions! Have a great day, Dayle Smith Department of Physics Whitman College ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problems with Jacobi diagonalization
Dayle Smith wrote: Thanks for your help, Justin. I ran gmxcheck -c topol.tpr (12284 atoms in file) and gmxcheck -f traj.xtc (# Atoms 29). The difference is Indeed, that's the problem, then! the SOL atoms. I made another .tpr file with xtcgroups = TDR SOL, and now gmxcheck shows that the number of atoms in topol.tpr is 12284, but I still can't get g_covar to work. Maybe these are unrelated problems, I'm not sure. You haven't really changed anything. The xtc-grps parameter defines what was saved in the simulation. Setting it after the fact does not affect the already-produced .xtc file. What you need is a .tpr file that contains only TDR, so you would have to make modifications to your .top in order to generate this TDR-only .tpr file. -Justin ~Dayle On Wed, Apr 1, 2009 at 2:49 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Dayle Smith wrote: Hi Tsjerk, Thank you for your quick and helpful response. I defined xtc_grps = TDR in my .mdp file (then I use grompp -f mdpme.mdp -c confout.gro -p topol.top -o topol.tpr -np 8 -n index.ndx, index contains TDR and SOL) and run it with -np 8. I'm afraid that I don't understand what shuffling or matching series refers to (a clue that I'm doing something wrong). This g_covar error message is probably another clue: WARNING: number of atoms in tpx (29) and trajectory (29) do not match --- Program g_covar, VERSION 3.3.3 Source code file: nrjac.c, line: 129 Fatal error: Error: Too many iterations in routine JACOBI So the # of atoms is the same, but some other key ingredient doesn't match. Can you please enlighten me?! I think the output error message is bizarre, but you still have a number of atoms in the .tpr that does not match the .xtc. If your simulation is of TDR and SOL, then those groups will be in your topol.tpr. If your xtc-grps specify only TDR, then there will be a coordinate mismatch. Run the following: gmxcheck -c topol.tpr gmxcheck -f traj.xtc and see if gmxcheck reports the same number of atoms in both files. This is the quickest way to know for sure. -Justin Thanks a lot, Dayle On Wed, Apr 1, 2009 at 11:12 AM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com mailto:tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hi Dayle, Errm, really, the only cases I know of this error to occur is when I had a mismatch between the reference and trajectory. Did you specify xtc-groups? Did you shuffle the system? How did you assert that you have matching series? Have you tried using the reference and the trajectory to convert (part of) the trajectory to .pdb and visualize? If all else fails, can you send (a link to) an archive containing a single frame from the trajectory and the reference? Cheers, Tsjerk 2009/4/1 Dayle Smith daylemariesm...@gmail.com mailto:daylemariesm...@gmail.com mailto:daylemariesm...@gmail.com mailto:daylemariesm...@gmail.com: Greetings--- I'm working with a DNA system, and all of the routines I've worked with that require Jacobi diagonalization (g_covar, g_rms, etc) fail with the Too many iterations in routine JACOBI error. I'm using gromacs-3.3.3 with ffamber99 on the NCSA Mercury cluster. I've searched the archives, and I've found several entries in which users are advised to check that the coordinates in the trajectory and structure files match (mine do). I've also tried running covariance analysis on a small ligand molecule, and I get the same error. I can get g_covar to work with -nofit, but then I can't run g_anaeig. I'm eagerly looking forward to your suggestions! Have a great day, Dayle Smith Department of Physics Whitman College -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post
Re: [gmx-users] Problems with Jacobi diagonalization
Justin A. Lemkul wrote: Dayle Smith wrote: Thanks for your help, Justin. I ran gmxcheck -c topol.tpr (12284 atoms in file) and gmxcheck -f traj.xtc (# Atoms 29). The difference is Indeed, that's the problem, then! the SOL atoms. I made another .tpr file with xtcgroups = TDR SOL, and now gmxcheck shows that the number of atoms in topol.tpr is 12284, but I still can't get g_covar to work. Maybe these are unrelated problems, I'm not sure. You haven't really changed anything. The xtc-grps parameter defines what was saved in the simulation. Setting it after the fact does not affect the already-produced .xtc file. What you need is a .tpr file that contains only TDR, so you would have to make modifications to your .top in order to generate this TDR-only .tpr file. Or use tpbconv - this is the other application for that utility. Mark ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problems with Jacobi diagonalization
Or rather than modifying the .top use tpbconv with an index file to generate a new .tpr Tom --On Wednesday, April 01, 2009 21:15:34 -0400 Justin A. Lemkul jalem...@vt.edu wrote: Dayle Smith wrote: Thanks for your help, Justin. I ran gmxcheck -c topol.tpr (12284 atoms in file) and gmxcheck -f traj.xtc (# Atoms 29). The difference is Indeed, that's the problem, then! the SOL atoms. I made another .tpr file with xtcgroups = TDR SOL, and now gmxcheck shows that the number of atoms in topol.tpr is 12284, but I still can't get g_covar to work. Maybe these are unrelated problems, I'm not sure. You haven't really changed anything. The xtc-grps parameter defines what was saved in the simulation. Setting it after the fact does not affect the already-produced .xtc file. What you need is a .tpr file that contains only TDR, so you would have to make modifications to your .top in order to generate this TDR-only .tpr file. -Justin ~Dayle On Wed, Apr 1, 2009 at 2:49 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Dayle Smith wrote: Hi Tsjerk, Thank you for your quick and helpful response. I defined xtc_grps = TDR in my .mdp file (then I use grompp -f mdpme.mdp -c confout.gro -p topol.top -o topol.tpr -np 8 -n index.ndx, index contains TDR and SOL) and run it with -np 8. I'm afraid that I don't understand what shuffling or matching series refers to (a clue that I'm doing something wrong). This g_covar error message is probably another clue: WARNING: number of atoms in tpx (29) and trajectory (29) do not match --- Program g_covar, VERSION 3.3.3 Source code file: nrjac.c, line: 129 Fatal error: Error: Too many iterations in routine JACOBI So the # of atoms is the same, but some other key ingredient doesn't match. Can you please enlighten me?! I think the output error message is bizarre, but you still have a number of atoms in the .tpr that does not match the .xtc. If your simulation is of TDR and SOL, then those groups will be in your topol.tpr. If your xtc-grps specify only TDR, then there will be a coordinate mismatch. Run the following: gmxcheck -c topol.tpr gmxcheck -f traj.xtc and see if gmxcheck reports the same number of atoms in both files. This is the quickest way to know for sure. -Justin Thanks a lot, Dayle On Wed, Apr 1, 2009 at 11:12 AM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com mailto:tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hi Dayle, Errm, really, the only cases I know of this error to occur is when I had a mismatch between the reference and trajectory. Did you specify xtc-groups? Did you shuffle the system? How did you assert that you have matching series? Have you tried using the reference and the trajectory to convert (part of) the trajectory to .pdb and visualize? If all else fails, can you send (a link to) an archive containing a single frame from the trajectory and the reference? Cheers, Tsjerk 2009/4/1 Dayle Smith daylemariesm...@gmail.com mailto:daylemariesm...@gmail.com mailto:daylemariesm...@gmail.com mailto:daylemariesm...@gmail.com: Greetings--- I'm working with a DNA system, and all of the routines I've worked with that require Jacobi diagonalization (g_covar, g_rms, etc) fail with the Too many iterations in routine JACOBI error. I'm using gromacs-3.3.3 with ffamber99 on the NCSA Mercury cluster. I've searched the archives, and I've found several entries in which users are advised to check that the coordinates in the trajectory and structure files match (mine do). I've also tried running covariance analysis on a small ligand molecule, and I get the same error. I can get g_covar to work with -nofit, but then I can't run g_anaeig. I'm eagerly looking forward to your suggestions! Have a great day, Dayle Smith Department of Physics Whitman College -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
Re: [gmx-users] Problems with Jacobi diagonalization
Thanks, Mark- I re-ran a short MD simulation with TDR as the only xtc group, and used tpbconv to create a .tpr file with only TDR (tpxout.tpr) and ran g_covar with an index.ndx that contains only TPR (just to be safe!), g_covar -f traj.xtc -s tpxout.tpr -ref -n index.ndx and I still get the Jacobi error: Choose a group for the least squares fit Group 0 ( TDR) has29 elements There is one group in the index Choose a group for the covariance analysis Group 0 ( TDR) has29 elements There is one group in the index Calculating the average structure ... Reading frame 0 time0.000 --- Program g_covar, VERSION 3.3.3 Source code file: nrjac.c, line: 129 Fatal error: Error: Too many iterations in routine JACOBI ~Dayle On Wed, Apr 1, 2009 at 6:22 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Justin A. Lemkul wrote: Dayle Smith wrote: Thanks for your help, Justin. I ran gmxcheck -c topol.tpr (12284 atoms in file) and gmxcheck -f traj.xtc (# Atoms 29). The difference is Indeed, that's the problem, then! the SOL atoms. I made another .tpr file with xtcgroups = TDR SOL, and now gmxcheck shows that the number of atoms in topol.tpr is 12284, but I still can't get g_covar to work. Maybe these are unrelated problems, I'm not sure. You haven't really changed anything. The xtc-grps parameter defines what was saved in the simulation. Setting it after the fact does not affect the already-produced .xtc file. What you need is a .tpr file that contains only TDR, so you would have to make modifications to your .top in order to generate this TDR-only .tpr file. Or use tpbconv - this is the other application for that utility. Mark ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
