[gmx-users] problem with append option while extending simulation
Dear All I'm running a simulation for 300 ns and I divided it into 6 production runs, each one for 50 ns using extending simulation commands: tpbconv_mpi -s run_50.tpr -extend 5 -o run1_50.tpr mpirun -np 48 mdrun_mpi -v -deffnm run1_50 -cpi run_50.cpt -append By using the -append option I expected to find the new output files appended to the old ones as mentioned in the documentation (I didn't modify anything in the old output files), but this doesn't happen, the data in the old output files are for 50 ns only! P.S. The gromacs module I use is : 4.6.5-goolf-1.4.10-hybrid Have I done anything wrong? Thanks in Advance -- 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] Error: 'mdrun_mpi' is not a GROMACS command.
Hi, I'm using same command but without gmx_mpi and it works. On 18 Aug 2015 14:09, anu chandra anu80...@gmail.com wrote: Dear Gromcas users, I just expericend an error while running mpi version of Gromcas on a 64 processors in a cluster. The command I used for running mdrun is as follows, mpirun -ppn 16 -np 64 gmx_mpi mdrun_mpi -cpi eq1.cpt -deffnm eq2 But, unfortunately the run terminated with following error message. Can anyone help me to figure out what is gone wrong here? --- Program: gmx_mpi, VERSION 5.0.5 Source file: src/gromacs/commandline/cmdlinemodulemanager.cpp (line 408) Function:gmx::CommandLineModuleInterface* gmx::CommandLineModuleManager::Impl::processCommonOptions(gmx::CommandLineCommonOptionsHolder*, int*, char***) Error in user input: --- Program: gmx_mpi, VERSION 5.0.5 Source file: src/gromacs/commandline/cmdlinemodulemanager.cpp (line 408) Function:gmx::CommandLineModuleInterface* gmx::CommandLineModuleManager::Impl::processCommonOptions(gmx::CommandLineCommonOptionsHolder*, int*, char***) Error in user input: 'mdrun_mpi' is not a GROMACS command. - Many thanks Anu -- 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.
[gmx-users] Extending simulation with modifing .mdp file
Hi. I want to extend a simulation by 5 ps, but also I want to change some parameters in the old mdp file, so I type (run.mdp is the modified file) : grompp_mpi -f run.mdp -c run_50.tpr -o run1_50.tpr tpbconv_mpi -s run_50.tpr -extend 5 -o run1_50.tpr mpirun -np 60 mdrun_mpi -v -deffnm run1_50 -cpi run_50.cpt -append Is this correct? Another question. I'm using nose-hoover thermostat and Parrinello-Rahman barostat in production run . Is using md integrator convenient? Thanks, Asma -- 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] High speed performance
Dr. Carsten Thank you so much :) On Tue, Aug 4, 2015 at 11:44 AM, Kutzner, Carsten ckut...@gwdg.de wrote: On 04 Aug 2015, at 00:02, Asmaa El khodary asma.moh_...@aucegypt.edu wrote: Yes, I’m running the simulation on a cluster using 5 computational nodes, In that case I would run on a single node with 8 cores first so that you can compare the parallel performance to a single node and can derive how high the parallel efficiency is. That will depend a lot on your network. This is worth the effort, as sometimes using less nodes results in higher performance :) Carsten each one has 8 cores, so the total number of cores is 40. The module I'm using is GROMACS/4.6.5-goolf-1.4.10-hybrid. On Tue, Aug 4, 2015 at 12:45 AM, Szilárd Páll pall.szil...@gmail.com wrote: 40 cores? Are you sure it's not two 10-core CPUs with HyperThreading = 2x20 threads supported? -- Szilárd On Mon, Aug 3, 2015 at 3:19 PM, Asmaa El khodary asma.moh_...@aucegypt.edu wrote: Dr Carsten Thank you so much for your reply. Yes, you are right, it's a 40 core CPU. I'm using 2 fs time step with Particle Mesh Ewald for long-range electrostatics. I've attached the parameter file I'm using for the production run. Best Regards Asma On Mon, Aug 3, 2015 at 4:03 PM, Asmaa El khodary asma.moh_...@aucegypt.edu wrote: Hi, I'm currently simulating a protein consists of 2776 atoms with 173 residues using CPU with 5 nodes, 40 core processors. The performance of the simulation is 70 ns per day (50 ns simulation takes almost 18 hours). Is this realistic or not? Thanks in Advance Asma -- 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. -- 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. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] High speed performance
Yes, I'm running the simulation on a cluster using 5 computational nodes, each one has 8 cores, so the total number of cores is 40. The module I'm using is GROMACS/4.6.5-goolf-1.4.10-hybrid. On Tue, Aug 4, 2015 at 12:45 AM, Szilárd Páll pall.szil...@gmail.com wrote: 40 cores? Are you sure it's not two 10-core CPUs with HyperThreading = 2x20 threads supported? -- Szilárd On Mon, Aug 3, 2015 at 3:19 PM, Asmaa El khodary asma.moh_...@aucegypt.edu wrote: Dr Carsten Thank you so much for your reply. Yes, you are right, it's a 40 core CPU. I'm using 2 fs time step with Particle Mesh Ewald for long-range electrostatics. I've attached the parameter file I'm using for the production run. Best Regards Asma On Mon, Aug 3, 2015 at 4:03 PM, Asmaa El khodary asma.moh_...@aucegypt.edu wrote: Hi, I'm currently simulating a protein consists of 2776 atoms with 173 residues using CPU with 5 nodes, 40 core processors. The performance of the simulation is 70 ns per day (50 ns simulation takes almost 18 hours). Is this realistic or not? Thanks in Advance Asma -- 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. -- 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] High speed performance
Hi, I'm currently simulating a protein consists of 2776 atoms with 173 residues using CPU with 5 nodes, 40 core processors. The performance of the simulation is 70 ns per day (50 ns simulation takes almost 18 hours). Is this realistic or not? Thanks in Advance Asma -- 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] High speed performance
Dr Carsten Thank you so much for your reply. Yes, you are right, it's a 40 core CPU. I'm using 2 fs time step with Particle Mesh Ewald for long-range electrostatics. I've attached the parameter file I'm using for the production run. Best Regards Asma On Mon, Aug 3, 2015 at 4:03 PM, Asmaa El khodary asma.moh_...@aucegypt.edu wrote: Hi, I'm currently simulating a protein consists of 2776 atoms with 173 residues using CPU with 5 nodes, 40 core processors. The performance of the simulation is 70 ns per day (50 ns simulation takes almost 18 hours). Is this realistic or not? Thanks in Advance Asma -- 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] Problem with gmx distance
Hi, I created an index files with two residue groups, 15 r 22 contains 15 atoms and 16 r 137 contains 24 atoms. Then, I use: gmx distance -s run.tpr -f run.xtc -n index.ndx -oall dist.xvg when I try to select both groups, I get this message Cannot match 'group 15', because no such index group can be found. Could you explain that error to me please? How to fix it? Thanks Asmaa -- 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.
