Re: [gmx-users] g_covar error in Gromacs 5
On 9/29/15 1:00 PM, Rebeca García Fandiño wrote: Hi, I am trying to use g_covar like this: echo 2 2 | g_covar -s prod_clus_1_exp.tpr -f prod_clus_exp_fit.xtc -n index_noH_exp.ndx -o eigenval_300K_exp.xvg -v eigenvect_300K_exp.trr In Gromacs 5.0.4 I get an error: (...) Choose a group for the least squares fit Group 0 ( System) has 4437 elements Group 1 ( Other) has 147 elements Group 2 (MOL) has 147 elements Select a group: 2 Selected 2: 'MOL' Choose a group for the covariance analysis Group 0 ( System) has 4437 elements Group 1 ( Other) has 147 elements Group 2 (MOL) has 147 elements Select a group: 2 Selected 2: 'MOL' Note: the fit and analysis group are identical, while the fit is mass weighted and the analysis is not. Making the fit non mass weighted. Calculating the average structure ... Reading frames from gro file 'frame t= 18.000', 4437 atoms. Last frame 0 time 18.000 Back Off! I just backed up average.pdb to ./#average.pdb.4# Constructing covariance matrix (441x441) ... Reading frames from gro file 'frame t= 18.000', 4437 atoms. Last frame 0 time 18.000 Read 1 frames Trace of the covariance matrix: 0 (nm^2) Diagonalizing ... Sum of the eigenvalues: 0 (nm^2) Violación de segmento That means "Segmentation fault". The most strange is that using Gromacs 4.6.2 this error does not appear, and the command executes properly. Could it be maybe a bug in Gromacs 5? Yes, one that was fixed after 5.0.4. When encountering potential bugs, always try upgrading to the latest version in your series (at least 5.0.6, if not 5.1) and try again. -Justin -- == 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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] g_covar error in Gromacs 5
Hi, I am trying to use g_covar like this: echo 2 2 | g_covar -s prod_clus_1_exp.tpr -f prod_clus_exp_fit.xtc -n index_noH_exp.ndx -o eigenval_300K_exp.xvg -v eigenvect_300K_exp.trr In Gromacs 5.0.4 I get an error: (...) Choose a group for the least squares fit Group 0 ( System) has 4437 elements Group 1 ( Other) has 147 elements Group 2 (MOL) has 147 elements Select a group: 2 Selected 2: 'MOL' Choose a group for the covariance analysis Group 0 ( System) has 4437 elements Group 1 ( Other) has 147 elements Group 2 (MOL) has 147 elements Select a group: 2 Selected 2: 'MOL' Note: the fit and analysis group are identical, while the fit is mass weighted and the analysis is not. Making the fit non mass weighted. Calculating the average structure ... Reading frames from gro file 'frame t= 18.000', 4437 atoms. Last frame 0 time 18.000 Back Off! I just backed up average.pdb to ./#average.pdb.4# Constructing covariance matrix (441x441) ... Reading frames from gro file 'frame t= 18.000', 4437 atoms. Last frame 0 time 18.000 Read 1 frames Trace of the covariance matrix: 0 (nm^2) Diagonalizing ... Sum of the eigenvalues: 0 (nm^2) Violación de segmento That means "Segmentation fault". The most strange is that using Gromacs 4.6.2 this error does not appear, and the command executes properly. Could it be maybe a bug in Gromacs 5? Thanks a lot for your help in advance. Dr. Rebeca Garcia Santiago de Compostela University (Spain) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] g_covar Segmentation fault problem
Dear gromacs user, In order to estimate system absolute entropy value I want to use g_covar + g_anaeig commands. However when I *'g_covar -f nvt.trr -s nvt.tpr'* I get a segmentation fault after *'Diagonalizing '* step from gromacs 4.6.6 and 5.0.3. *Constructing covariance matrix (12258x12258) ...Last frame 4000 time 4000.000 Read 4001 framesTrace of the covariance matrix: 12454.6 (nm^2)Diagonalizing ...Sum of the eigenvalues: 12454.6 (nm^2)Segmentation fault (core dumped)* But the same command, executed with g_covar of gromacs 4.6.3 works without any error or fault. Was it a bug and corrected for newer versions? I saw the release note of * 'Fixed a complicated bug in g_anaeig and g_covar, if the number of frames for a covariance analysis is fewer than the number of degrees of freedom' *for gromacs 4.6.6. Do I need to lower the number of atoms to analyze or higher the frame numbers or is it ok if I use 4.6.3? Thanks. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_covar Segmentation fault problem
On 7/16/15 12:26 PM, gozde ergin wrote: Thank for reply Justin but I have difficulty to understand which version has this bug? If 'Segmentation fault because of #DOF and frames numbers difference' is a bug than gromacs 4.6.3 is working correctly, right? Offhand, I don't know which outdated versions work and which don't. To be safe: 4.6.x series, use version = 4.6.6 5.0.x series, use version 5.0.5 Any other version in the development repo (master, release-5-0, etc) -Justin On Thu, Jul 16, 2015 at 6:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/15 10:22 AM, gozde ergin wrote: Dear gromacs user, In order to estimate system absolute entropy value I want to use g_covar + g_anaeig commands. However when I *'g_covar -f nvt.trr -s nvt.tpr'* I get a segmentation fault after *'Diagonalizing '* step from gromacs 4.6.6 and 5.0.3. *Constructing covariance matrix (12258x12258) ...Last frame 4000 time 4000.000 Read 4001 framesTrace of the covariance matrix: 12454.6 (nm^2)Diagonalizing ...Sum of the eigenvalues: 12454.6 (nm^2)Segmentation fault (core dumped)* But the same command, executed with g_covar of gromacs 4.6.3 works without any error or fault. Was it a bug and corrected for newer versions? I saw the release note of * 'Fixed a complicated bug in g_anaeig and g_covar, if the number of frames for a covariance analysis is fewer than the number of degrees of freedom' *for gromacs 4.6.6. The bug was also fixed for 5.0.5. -Justin -- == 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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == 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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_covar Segmentation fault problem
Ok by using version 4.6.6 I got this segmentation fault error which means number of frames should be equal or bigger than the number of degrees of freedom. On Thu, Jul 16, 2015 at 7:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/15 12:26 PM, gozde ergin wrote: Thank for reply Justin but I have difficulty to understand which version has this bug? If 'Segmentation fault because of #DOF and frames numbers difference' is a bug than gromacs 4.6.3 is working correctly, right? Offhand, I don't know which outdated versions work and which don't. To be safe: 4.6.x series, use version = 4.6.6 5.0.x series, use version 5.0.5 Any other version in the development repo (master, release-5-0, etc) -Justin On Thu, Jul 16, 2015 at 6:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/15 10:22 AM, gozde ergin wrote: Dear gromacs user, In order to estimate system absolute entropy value I want to use g_covar + g_anaeig commands. However when I *'g_covar -f nvt.trr -s nvt.tpr'* I get a segmentation fault after *'Diagonalizing '* step from gromacs 4.6.6 and 5.0.3. *Constructing covariance matrix (12258x12258) ...Last frame 4000 time 4000.000 Read 4001 framesTrace of the covariance matrix: 12454.6 (nm^2)Diagonalizing ...Sum of the eigenvalues: 12454.6 (nm^2)Segmentation fault (core dumped)* But the same command, executed with g_covar of gromacs 4.6.3 works without any error or fault. Was it a bug and corrected for newer versions? I saw the release note of * 'Fixed a complicated bug in g_anaeig and g_covar, if the number of frames for a covariance analysis is fewer than the number of degrees of freedom' *for gromacs 4.6.6. The bug was also fixed for 5.0.5. -Justin -- == 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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == 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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_covar Segmentation fault problem
On 7/16/15 1:09 PM, gozde ergin wrote: Ok by using version 4.6.6 I got this segmentation fault error which means number of frames should be equal or bigger than the number of degrees of freedom. Then use 4.6.7. Maybe my = should have been instead. The best bet when you get failures like this is to always upgrade to the latest version in whatever series you're trying to use. 4.6.7 should work. If not, 5.0.5 definitely does. -Justin On Thu, Jul 16, 2015 at 7:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/15 12:26 PM, gozde ergin wrote: Thank for reply Justin but I have difficulty to understand which version has this bug? If 'Segmentation fault because of #DOF and frames numbers difference' is a bug than gromacs 4.6.3 is working correctly, right? Offhand, I don't know which outdated versions work and which don't. To be safe: 4.6.x series, use version = 4.6.6 5.0.x series, use version 5.0.5 Any other version in the development repo (master, release-5-0, etc) -Justin On Thu, Jul 16, 2015 at 6:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/15 10:22 AM, gozde ergin wrote: Dear gromacs user, In order to estimate system absolute entropy value I want to use g_covar + g_anaeig commands. However when I *'g_covar -f nvt.trr -s nvt.tpr'* I get a segmentation fault after *'Diagonalizing '* step from gromacs 4.6.6 and 5.0.3. *Constructing covariance matrix (12258x12258) ...Last frame 4000 time 4000.000 Read 4001 framesTrace of the covariance matrix: 12454.6 (nm^2)Diagonalizing ...Sum of the eigenvalues: 12454.6 (nm^2)Segmentation fault (core dumped)* But the same command, executed with g_covar of gromacs 4.6.3 works without any error or fault. Was it a bug and corrected for newer versions? I saw the release note of * 'Fixed a complicated bug in g_anaeig and g_covar, if the number of frames for a covariance analysis is fewer than the number of degrees of freedom' *for gromacs 4.6.6. The bug was also fixed for 5.0.5. -Justin -- == 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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == 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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == 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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_covar Segmentation fault problem
Thank for reply Justin but I have difficulty to understand which version has this bug? If 'Segmentation fault because of #DOF and frames numbers difference' is a bug than gromacs 4.6.3 is working correctly, right? On Thu, Jul 16, 2015 at 6:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/15 10:22 AM, gozde ergin wrote: Dear gromacs user, In order to estimate system absolute entropy value I want to use g_covar + g_anaeig commands. However when I *'g_covar -f nvt.trr -s nvt.tpr'* I get a segmentation fault after *'Diagonalizing '* step from gromacs 4.6.6 and 5.0.3. *Constructing covariance matrix (12258x12258) ...Last frame 4000 time 4000.000 Read 4001 framesTrace of the covariance matrix: 12454.6 (nm^2)Diagonalizing ...Sum of the eigenvalues: 12454.6 (nm^2)Segmentation fault (core dumped)* But the same command, executed with g_covar of gromacs 4.6.3 works without any error or fault. Was it a bug and corrected for newer versions? I saw the release note of * 'Fixed a complicated bug in g_anaeig and g_covar, if the number of frames for a covariance analysis is fewer than the number of degrees of freedom' *for gromacs 4.6.6. The bug was also fixed for 5.0.5. -Justin -- == 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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_covar Segmentation fault problem
On 7/16/15 10:22 AM, gozde ergin wrote: Dear gromacs user, In order to estimate system absolute entropy value I want to use g_covar + g_anaeig commands. However when I *'g_covar -f nvt.trr -s nvt.tpr'* I get a segmentation fault after *'Diagonalizing '* step from gromacs 4.6.6 and 5.0.3. *Constructing covariance matrix (12258x12258) ...Last frame 4000 time 4000.000 Read 4001 framesTrace of the covariance matrix: 12454.6 (nm^2)Diagonalizing ...Sum of the eigenvalues: 12454.6 (nm^2)Segmentation fault (core dumped)* But the same command, executed with g_covar of gromacs 4.6.3 works without any error or fault. Was it a bug and corrected for newer versions? I saw the release note of * 'Fixed a complicated bug in g_anaeig and g_covar, if the number of frames for a covariance analysis is fewer than the number of degrees of freedom' *for gromacs 4.6.6. The bug was also fixed for 5.0.5. -Justin -- == 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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] g_covar
Hi, I need help please. I am calculating entropy of a single water in water solution. So I did a 10 ns NPT. Then I run g_covar -f NPT.xtc -s NPT.tpr -o -l -av -v and g_anaeig_d -v eigenvec.trr -entropy -eig eigenval.xvg I have two questions. 1- In the g_covar it asks to select group, should I choose 'system' for both asks, or choose a 'single water'? 2- When I choose different time frames (of course after equilibrium), I get completely different entropy, why is that so? Best regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] g_covar + g_anaeig entropy calculation
Hello: I am trying to calculate ligand binding energy for protein/ligand system. The enthapy part was done by GMXPBSA. Now I would like to evalutate the entropy part with g_covar + g_anaeig. Here I got some questions: --- is it necessary using double precison Gromacs for entropy evaluation? --- I googled a lot concering on this topic from Gromacs mailist. If I understand correctly, we should (1) generate eigenvec.trr as input file for g_anaeig (2) use g_anaeig calculate the entropy is it correct? ---I am trying to run command: g_covar -f input.xtc -s input.tpr -n -o eigenval.xvg -v eigenvec.trr -av average.pdb -l covar.log -ascii covar.dat -xpm covar.xpm -xpma covara.xpm The trajecotry I am using for above commend was extracted from MD simulations and water/ions were removed from the system. When g_covar pop up a dialoug asking which compoenent I am going to analyze, I selected System which contains protien+ligand Is it correct to do so? ---I am planning to run g_anaeig with following command for entropy evaluation: g_anaeig -v eigenvec.trr -entropy -s input.tpr -comp Shall I speicify additional options for this purpose? Thank you very much. Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] g_covar
Dear users in my anslysis ,i did g_covar and encountered to this note: (the fit and anslysis group are identical while the fit is mass weighted and the analysis is not making the fit non mass weighted) is this important note or not? thanks for your reply -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_covar
Hey :) Depends on what you're doing exactly and why. If you're only using C's, it doesn't matter. Likewise, for C/N/O the differences are not that large. On top of that, if you use PCA as a geometrical analysis (not interested in eigenfrequencies), then it also doesn't matter a great deal. Hope it helps, Tsjerk On Mon, May 19, 2014 at 11:02 AM, elham tazikeh elham.tazi...@gmail.comwrote: Dear users in my anslysis ,i did g_covar and encountered to this note: (the fit and anslysis group are identical while the fit is mass weighted and the analysis is not making the fit non mass weighted) is this important note or not? thanks for your reply -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] g_covar warnings
Hello everyone, The documentation reads: All structures are fitted to the structure in the structure file. When this is not a run input file periodicity will not be taken into account. This is rather cryptic, what does it mean in practice? No tpr, no party? What if I use a properly centered and whole .gro file? When ran with a .gro as the structure input file, I get two warnings. One is related to the masses, which are non-existent in the .gro, but I don't need them anyway. The second warning is honestly confusing me even more. WARNING: If there are molecules in the input trajectory file that are broken across periodic boundaries, they cannot be made whole (or treated as whole) without you providing a run input file. The documentation points out to the structure input file and now it's the trajectory? What's going on? Do I also need to make each frame whole in the input .xtc? Can someone elaborate on this? Thank you in advance, Best regards, João Henriques -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_covar warnings
Thanks Justin. That corroborates my no .tpr, no party suspicion. However, would it be possible to achieve a correct analysis if I were to use a whole .gro with a properly pre-processed .xtc (-ur -pbc)? Maybe I didn't explain myself properly, but that's what I want to know. /J On Thu, Mar 27, 2014 at 6:32 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/27/14, 1:27 PM, João Henriques wrote: Hello everyone, The documentation reads: All structures are fitted to the structure in the structure file. When this is not a run input file periodicity will not be taken into account. This is rather cryptic, what does it mean in practice? No tpr, no party? What if I use a properly centered and whole .gro file? When ran with a .gro as the structure input file, I get two warnings. One is related to the masses, which are non-existent in the .gro, but I don't need them anyway. The second warning is honestly confusing me even more. WARNING: If there are molecules in the input trajectory file that are broken across periodic boundaries, they cannot be made whole (or treated as whole) without you providing a run input file. The documentation points out to the structure input file and now it's the trajectory? What's going on? Do I also need to make each frame whole in the input .xtc? Can someone elaborate on this? The documentation consistently refers to the run input file. A .tpr has record of how periodicity is treated. Nothing else does. If you don't tell g_covar (like most Gromacs tools) how periodicity is treated, you can get garbage as a result. The trajectory may have broken molecules, because mdrun doesn't care how they look - it has a run input file and thus knowledge of periodicity. When running analysis like g_covar, if the bonded connectivity of the molecule and the periodicity are unknown (again, if you're not using a .tpr), then absolute displacements of coordinates are used, thus your analysis might be totally hosed if the molecule splits - that would be a rather dramatic structure change detected by g_covar. In fact, so dramatic that it's false. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_covar warnings
On 3/27/14, 1:54 PM, João Henriques wrote: Thanks Justin. That corroborates my no .tpr, no party suspicion. However, would it be possible to achieve a correct analysis if I were to use a whole .gro with a properly pre-processed .xtc (-ur -pbc)? Maybe I didn't explain myself properly, but that's what I want to know. Yes, if you have removed jumps and have intact structures throughout the trajectory, you're fine. The warning is only there for users who haven't thought ahead. -Justin /J On Thu, Mar 27, 2014 at 6:32 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/27/14, 1:27 PM, João Henriques wrote: Hello everyone, The documentation reads: All structures are fitted to the structure in the structure file. When this is not a run input file periodicity will not be taken into account. This is rather cryptic, what does it mean in practice? No tpr, no party? What if I use a properly centered and whole .gro file? When ran with a .gro as the structure input file, I get two warnings. One is related to the masses, which are non-existent in the .gro, but I don't need them anyway. The second warning is honestly confusing me even more. WARNING: If there are molecules in the input trajectory file that are broken across periodic boundaries, they cannot be made whole (or treated as whole) without you providing a run input file. The documentation points out to the structure input file and now it's the trajectory? What's going on? Do I also need to make each frame whole in the input .xtc? Can someone elaborate on this? The documentation consistently refers to the run input file. A .tpr has record of how periodicity is treated. Nothing else does. If you don't tell g_covar (like most Gromacs tools) how periodicity is treated, you can get garbage as a result. The trajectory may have broken molecules, because mdrun doesn't care how they look - it has a run input file and thus knowledge of periodicity. When running analysis like g_covar, if the bonded connectivity of the molecule and the periodicity are unknown (again, if you're not using a .tpr), then absolute displacements of coordinates are used, thus your analysis might be totally hosed if the molecule splits - that would be a rather dramatic structure change detected by g_covar. In fact, so dramatic that it's false. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_covar warnings
Great, that's what I needed to know. Still, I totally agree with you. There are certain best practices, and using a .tpr is always the best choice. Thanks, João On Thu, Mar 27, 2014 at 7:02 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/27/14, 1:54 PM, João Henriques wrote: Thanks Justin. That corroborates my no .tpr, no party suspicion. However, would it be possible to achieve a correct analysis if I were to use a whole .gro with a properly pre-processed .xtc (-ur -pbc)? Maybe I didn't explain myself properly, but that's what I want to know. Yes, if you have removed jumps and have intact structures throughout the trajectory, you're fine. The warning is only there for users who haven't thought ahead. -Justin /J On Thu, Mar 27, 2014 at 6:32 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/27/14, 1:27 PM, João Henriques wrote: Hello everyone, The documentation reads: All structures are fitted to the structure in the structure file. When this is not a run input file periodicity will not be taken into account. This is rather cryptic, what does it mean in practice? No tpr, no party? What if I use a properly centered and whole .gro file? When ran with a .gro as the structure input file, I get two warnings. One is related to the masses, which are non-existent in the .gro, but I don't need them anyway. The second warning is honestly confusing me even more. WARNING: If there are molecules in the input trajectory file that are broken across periodic boundaries, they cannot be made whole (or treated as whole) without you providing a run input file. The documentation points out to the structure input file and now it's the trajectory? What's going on? Do I also need to make each frame whole in the input .xtc? Can someone elaborate on this? The documentation consistently refers to the run input file. A .tpr has record of how periodicity is treated. Nothing else does. If you don't tell g_covar (like most Gromacs tools) how periodicity is treated, you can get garbage as a result. The trajectory may have broken molecules, because mdrun doesn't care how they look - it has a run input file and thus knowledge of periodicity. When running analysis like g_covar, if the bonded connectivity of the molecule and the periodicity are unknown (again, if you're not using a .tpr), then absolute displacements of coordinates are used, thus your analysis might be totally hosed if the molecule splits - that would be a rather dramatic structure change detected by g_covar. In fact, so dramatic that it's false. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
