Re: [gmx-users] No convergence with g_nmeig
Dear gromacs users, I still have the same problem with the vector convergence. There is a link with the size of my protein (18 081 atoms) ? I tried with a small molecule composed with 826 atoms and it seems to work. Any idea, please. Best Esra Hi, Thank you for your response. I used a supercomputer and all tools are compiled with mpi, I used 1 cpu and I have also the same result. Best, Esra Message: 2 Date: Thu, 5 Nov 2015 14:45:27 + From: Joaquim Rui de Castro Rodrigues http://gmane.org/get-address.php?address=joaquim.rodrigues%2d7rSwZE0QHb3QUPosyRRdSA%40public.gmane.org>> To: "gmx-users@...<http://gmane.org/get-address.php?address=gmx%2dusers%2d0nhw1vs2%2b5JAfugRpC6u6w%40public.gmane.org>" http://gmane.org/get-address.php?address=gmx%2dusers%2d0nhw1vs2%2b5JAfugRpC6u6w%40public.gmane.org>> Subject: Re: [gmx-users] No convergence with g_nmeig Message-ID: <99DCD30D03D1124CBDFCE15D7659B63183F0AA9A75@...<http://gmane.org/get-address.php?address=99DCD30D03D1124CBDFCE15D7659B63183F0AA9A75%2dTBb6hYIbNRuPJ8G44WGNSF6hYfS7NtTn%40public.gmane.org>> Content-Type: text/plain; charset="us-ascii" Hi, You seem to be running the calculation in parallel (g_nmeig_mpi_d). I don't think this is possible. Have you tried the nmeig serial version? HTH, Rui Rodrigues De: gromacs.org_gmx-users-bounces@...<http://gmane.org/get-address.php?address=gromacs.org%5fgmx%2dusers%2dbounces%2dmrEvjEli4ZDCMOUXqa3p%2bTAV6s6igYVG%40public.gmane.org> [gromacs.org_gmx-users-bounces@...<http://gmane.org/get-address.php?address=gromacs.org%5fgmx%2dusers%2dbounces%2dmrEvjEli4ZDCMOUXqa3p%2bTAV6s6igYVG%40public.gmane.org>] Em Nome De KARAKAS Esra [Esra.Karakas@...<http://gmane.org/get-address.php?address=Esra.Karakas%2dKCE40YydGKI%40public.gmane.org>] Enviado: quinta-feira, 5 de Novembro de 2015 11:08 Para: gromacs.org_gmx-users@...<http://gmane.org/get-address.php?address=gromacs.org%5fgmx%2dusers%2dmrEvjEli4ZDCMOUXqa3p%2bTAV6s6igYVG%40public.gmane.org> Assunto: Re: [gmx-users] No convergence with g_nmeig Any idea, please. Best Esra KARAKAS Dear gromacs users, I am trying to diagonalize my Hessian matrix obtained from mdrun (normal mode calulation) but I have this message and my vector 1 doesn't converge : GROMACS: gmx nmeig, VERSION 5.0.4 (double precision) Executable: /usr/local/gromacs-5.0.4/bin/gmx_mpi_d Library dir: /usr/local/gromacs-5.0.4/share/gromacs/top Command line: g_nmeig_mpi_d -s nm.tpr -f nm.mtx -v eigenvec_TEST -of eigenfreq_TEST -ol eigenval_TEST Reading file nm.tpr, VERSION 5.0.4 (double precision) Reading file nm.tpr, VERSION 5.0.4 (double precision) Reading double precision matrix generated by Gromacs VERSION 5.0.4 Diagonalizing to find eigenvectors 1 through 50... Calculation Ritz values and Lanczos vectors, max 1000 iterations... ^MIteration1: 0 out of 50 Ritz values converged.^MIteration2: 0 out of 50 Ritz values converged.^MIteration3: 0 out of 50 Ritz values converged. I found a similar problem on the gmx-users but any response https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2006-February/020179.html Do you know why my vector 1 doesn't converge ? Best regards, Esra KARAKAS -- 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] No convergence with g_nmeig
Hi, Thank you for your response. I used a supercomputer and all tools are compiled with mpi, I used 1 cpu and I have also the same result. Best, Esra Message: 2 Date: Thu, 5 Nov 2015 14:45:27 + From: Joaquim Rui de Castro Rodrigues To: "gmx-us...@gromacs.org" Subject: Re: [gmx-users] No convergence with g_nmeig Message-ID: <99dcd30d03d1124cbdfce15d7659b63183f0aa9...@mbx03.ipleiria.pt> Content-Type: text/plain; charset="us-ascii" Hi, You seem to be running the calculation in parallel (g_nmeig_mpi_d). I don't think this is possible. Have you tried the nmeig serial version? HTH, Rui Rodrigues De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Em Nome De KARAKAS Esra [esra.kara...@cea.fr] Enviado: quinta-feira, 5 de Novembro de 2015 11:08 Para: gromacs.org_gmx-users@maillist.sys.kth.se Assunto: Re: [gmx-users] No convergence with g_nmeig Any idea, please. Best Esra KARAKAS Dear gromacs users, I am trying to diagonalize my Hessian matrix obtained from mdrun (normal mode calulation) but I have this message and my vector 1 doesn't converge : GROMACS: gmx nmeig, VERSION 5.0.4 (double precision) Executable: /usr/local/gromacs-5.0.4/bin/gmx_mpi_d Library dir: /usr/local/gromacs-5.0.4/share/gromacs/top Command line: g_nmeig_mpi_d -s nm.tpr -f nm.mtx -v eigenvec_TEST -of eigenfreq_TEST -ol eigenval_TEST Reading file nm.tpr, VERSION 5.0.4 (double precision) Reading file nm.tpr, VERSION 5.0.4 (double precision) Reading double precision matrix generated by Gromacs VERSION 5.0.4 Diagonalizing to find eigenvectors 1 through 50... Calculation Ritz values and Lanczos vectors, max 1000 iterations... ^MIteration1: 0 out of 50 Ritz values converged.^MIteration2: 0 out of 50 Ritz values converged.^MIteration3: 0 out of 50 Ritz values converged. I found a similar problem on the gmx-users but any response https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2006-February/020179.html Do you know why my vector 1 doesn't converge ? Best regards, Esra KARAKAS -- 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] No convergence with g_nmeig
Any idea, please. Best Esra KARAKAS Dear gromacs users, I am trying to diagonalize my Hessian matrix obtained from mdrun (normal mode calulation) but I have this message and my vector 1 doesn't converge : GROMACS: gmx nmeig, VERSION 5.0.4 (double precision) Executable: /usr/local/gromacs-5.0.4/bin/gmx_mpi_d Library dir: /usr/local/gromacs-5.0.4/share/gromacs/top Command line: g_nmeig_mpi_d -s nm.tpr -f nm.mtx -v eigenvec_TEST -of eigenfreq_TEST -ol eigenval_TEST Reading file nm.tpr, VERSION 5.0.4 (double precision) Reading file nm.tpr, VERSION 5.0.4 (double precision) Reading double precision matrix generated by Gromacs VERSION 5.0.4 Diagonalizing to find eigenvectors 1 through 50... Calculation Ritz values and Lanczos vectors, max 1000 iterations... ^MIteration1: 0 out of 50 Ritz values converged.^MIteration2: 0 out of 50 Ritz values converged.^MIteration3: 0 out of 50 Ritz values converged. I found a similar problem on the gmx-users but any response https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2006-February/020179.html Do you know why my vector 1 doesn't converge ? Best regards, Esra KARAKAS -- 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] No convergence with g_nmeig
Dear gromacs users, I am trying to diagonalize my Hessian matrix obtained from mdrun (normal mode calulation) but I have this message and my vector 1 doesn't converge : GROMACS: gmx nmeig, VERSION 5.0.4 (double precision) Executable: /usr/local/gromacs-5.0.4/bin/gmx_mpi_d Library dir: /usr/local/gromacs-5.0.4/share/gromacs/top Command line: g_nmeig_mpi_d -s nm.tpr -f nm.mtx -v eigenvec_TEST -of eigenfreq_TEST -ol eigenval_TEST Reading file nm.tpr, VERSION 5.0.4 (double precision) Reading file nm.tpr, VERSION 5.0.4 (double precision) Reading double precision matrix generated by Gromacs VERSION 5.0.4 Diagonalizing to find eigenvectors 1 through 50... Calculation Ritz values and Lanczos vectors, max 1000 iterations... ^MIteration1: 0 out of 50 Ritz values converged.^MIteration2: 0 out of 50 Ritz values converged.^MIteration3: 0 out of 50 Ritz values converged. I found a similar problem on the gmx-users but any response https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2006-February/020179.html Do you know why my vector 1 doesn't converge ? Best regards, Esra KARAKAS -- 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] NMA run problem
Dear Gromacs Users, I am trying to run a Normal Mode Analysis with Gromacs v5.0.4 of a structure of 18081 atoms (without water) and I have a problem. I did a several minimization of my structure (1 SD, 1 CD and 4 L-BFGS), and everything went well. You can see below the relative informations for my last L-BFGS minimization: -- At the top of my .log file: Using 10 BFGS correction steps. F-max = 9.76934e-06 on atom 15076 F-Norm= 7.50769e-07 -- At the end of my .log file: Low-Memory BFGS Minimizer converged to Fmax < 1e-07 in 132449 steps Potential Energy = -9.52896691013964e+04 Maximum force = 9.82970751734797e-08 on atom 17063 Norm of force = 1.69009515334513e-08 then, when I run my NMA, I see this message in my .log file: Maximum force: 2.85412e+02 The force is probably not small enough to ensure that you are at a minimum. Be aware that negative eigenvalues may occur when the resulting matrix is diagonalized. My command line is : grompp_mpi_d -f nma.mdp -c em_BFGS_4_NoWater.gro -t em_BFGS_4_NoWater.trr -e em_BFGS_4_NoWater.edr -p protein.top -o nma_NoWater.tpr My question is why I have such a large force ? Thank you in advance for your help. -- 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.
