[gmx-users] Fatal Error: Residue 'DMP' not found in residue topology database
Hi guys, The error I'm getting is as follows All occupancies are one Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtypes.atp Atomtype 1 Reading residue database... (oplsaa) Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.rtp Residue 56 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb Processing chain 1 'A' (46 atoms, 1 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Warning: Starting residue DMP1 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.5.3 Source code file: resall.c, line: 581 Fatal error: Residue 'DMP' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- And this is the command I used pdb2gmx -f dmpc.pdb -o processed.gro -water spce -ignh Force field : OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) Help me solve this. Thanks and Regards Santhosh. - Santhosh Kumar Nagarajan MTech Bioinformatics SRM University Chennai India -- View this message in context: http://gromacs.5086.x6.nabble.com/Fatal-Error-Residue-DMP-not-found-in-residue-topology-database-tp5011333.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] RE: MPI runs on a local computer
Hi, Looks like my questions may be too much detailed. Hope someone could give some suggestions. If there is a more appropriate List where I should ask these questions, I will appreciate if anyone could let me know. Thanks again, Jianqing -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Xu, Jianqing Sent: 19 September 2013 13:49 To: gmx-users@gromacs.org Subject: [gmx-users] MPI runs on a local computer Dear all, I am learning the parallelization issues from the instructions on Gromacs website. I guess I got a rough understanding of MPI, thread-MPI, OpenMP. But I hope to get some advice about a correct way to run jobs. Say I have a local desktop having 16 cores. If I just want to run jobs on one computer or a single node (but multiple cores), I understand that I don't have to install and use OpenMPI, as Gromacs has its own thread-MPI included already and it should be good enough to run jobs on one machine. However, for some reasons, OpenMPI has already been installed on my machine, and I compiled Gromacs with it by using the flag: -DGMX_MPI=ON. My questions are: 1. Can I still use this executable (mdrun_mpi, built with OpenMPI library) to run multi-core jobs on my local desktop? Or the default Thread-MPI is actually a better option for a single computer or single node (but multi-cores) for whatever reasons? 2. Assuming I can still use this executable, let's say I want to use half of the cores (8 cores) on my machine to run a job, mpirun -np 8 mdrun_mpi -v -deffnm md a). Since I am not using all the cores, do I still need to lock the physical cores to use for better performance? Something like -nt for Thread-MPI? Or it is not necessary? b). For running jobs on a local desktop, or single node having ... say 16 cores, or even 64 cores, should I turn off the separate PME nodes (-npme 0)? Or it is better to leave as is? 3. If I want to run two different projects on my local desktop, say one project takes 8 cores, the other takes 4 cores (assuming I have enough memory), I just submit the jobs twice on my desktop: nohup mpirun -np 8 mdrun_mpi -v -deffnm md1 log1 nohup mpirun -np 4 mdrun_mpi -v -deffnm md2 log2 Will this be acceptable ? Will two jobs be competing the resource and eventually affect the performance? Sorry for so many detailed questions, but your help on this will be highly appreciated! Thanks a lot, Jianqing -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] MPI runs on a local computer
Hi Jianqing, On Sep 19, 2013, at 2:48 PM, Xu, Jianqing x...@medimmune.com wrote: Say I have a local desktop having 16 cores. If I just want to run jobs on one computer or a single node (but multiple cores), I understand that I don't have to install and use OpenMPI, as Gromacs has its own thread-MPI included already and it should be good enough to run jobs on one machine. However, for some reasons, OpenMPI has already been installed on my machine, and I compiled Gromacs with it by using the flag: -DGMX_MPI=ON. My questions are: 1. Can I still use this executable (mdrun_mpi, built with OpenMPI library) to run multi-core jobs on my local desktop? Or the default Thread-MPI is actually a better option for a single computer or single node (but multi-cores) for whatever reasons? You can either use OpenMPI or Gromacs build-in thread MPI library. If you only want to run on a single machine, I would recommend recompiling with thread-MPI, because this is in many cases a bit faster. 2. Assuming I can still use this executable, let's say I want to use half of the cores (8 cores) on my machine to run a job, mpirun -np 8 mdrun_mpi -v -deffnm md a). Since I am not using all the cores, do I still need to lock the physical cores to use for better performance? Something like -nt for Thread-MPI? Or it is not necessary? Depends on whether you get good scaling or not. Compare to a run on 1 core, for large systems the 4 or 8 core parallel runs should be (nearly) 4 or 8 times as fast. If that is the case, you do not need to worry about pinning. b). For running jobs on a local desktop, or single node having ... say 16 cores, or even 64 cores, should I turn off the separate PME nodes (-npme 0)? Or it is better to leave as is? You may want to check with g_tune_pme. Note that the optimum will depend on your system, and for each MD system you should find that out. 3. If I want to run two different projects on my local desktop, say one project takes 8 cores, the other takes 4 cores (assuming I have enough memory), I just submit the jobs twice on my desktop: nohup mpirun -np 8 mdrun_mpi -v -deffnm md1 log1 nohup mpirun -np 4 mdrun_mpi -v -deffnm md2 log2 Will this be acceptable ? Will two jobs be competing the resource and eventually affect the performance? Make some quick test runs (over a couple of minutes). Then you can check the performance of your 8 core run with and without another simulation running. Best, Carsten Sorry for so many detailed questions, but your help on this will be highly appreciated! Thanks a lot, Jianqing To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Fatal Error: Residue 'DMP' not found in residue topology database
On 9/20/13 2:28 AM, Santhosh Kumar Nagarajan wrote: Hi guys, The error I'm getting is as follows All occupancies are one Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtypes.atp Atomtype 1 Reading residue database... (oplsaa) Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.rtp Residue 56 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb Processing chain 1 'A' (46 atoms, 1 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Warning: Starting residue DMP1 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.5.3 Source code file: resall.c, line: 581 Fatal error: Residue 'DMP' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- And this is the command I used pdb2gmx -f dmpc.pdb -o processed.gro -water spce -ignh Force field : OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: grompp for minimization: note warning
Dear Tsjerk Thanks for your reply Before correcting the gro file, I knew that gro file is fixed format. I did this correction very carefully. Part of the gro file before and after correction is as follows: - before: - 14DOPCN4 755 0.260 1.726 6.354 14DOPCC5 756 0.263 1.741 6.204 14DOPCC1 757 0.136 1.777 6.423 14DOPCC2 758 0.279 1.580 6.384 14DOPCC3 759 0.383 1.799 6.403 14DOPCC6 760 0.386 1.685 6.132 14DOPCP8 761 0.628 1.683 6.064 14DOPC OM9 762 0.640 1.548 6.123 14DOPC OM10 763 0.747 1.771 6.072 14DOPC OS7 764 0.511 1.755 6.145 14DOPC OS11 765 0.576 1.681 5.913 14DOPC C12 766 0.591 1.806 5.845 14DOPC C13 767 0.470 1.901 5.846 14DOPC OS14 768 0.364 1.830 5.782 14DOPC C15 769 0.247 1.869 5.833 14DOPC O16 770 0.238 1.946 5.927 14DOPC C17 771 0.123 1.815 5.762 14DOPC C34 772 0.490 2.037 5.777 14DOPC OS35 773 0.541 2.029 5.644 14DOPC C36 774 0.591 2.142 5.593 14DOPC O37 775 0.595 2.252 5.646 14DOPC C38 776 0.674 2.092 5.476 14DOPC C18 777 -0.004 1.897 5.786 14DOPC C19 778 -0.138 1.837 5.744 14DOPC C20 779 -0.147 1.817 5.593 14DOPC C21 780 -0.196 1.678 5.552 14DOPC C22 781 -0.181 1.637 5.406 14DOPC C23 782 -0.252 1.722 5.301 14DOPC C24 783 -0.241 1.664 5.163 14DOPC C25 784 -0.267 1.738 5.054 14DOPC C26 785 -0.312 1.881 5.044 14DOPC C27 786 -0.368 1.918 4.907 14DOPC C28 787 -0.266 1.941 4.795 14DOPC C29 788 -0.324 2.015 4.674 14DOPC C30 789 -0.377 1.920 4.567 14DOPC C31 790 -0.377 1.984 4.428 14DOPC C32 791 -0.439 1.894 4.321 14DOPC C33 792 -0.358 1.890 4.191 14DOPC C39 793 0.818 2.145 5.475 14DOPC C40 794 0.906 2.056 5.387 14DOPC C41 795 1.042 2.123 5.364 14DOPC C42 796 1.160 2.029 5.339 14DOPC C43 797 1.136 1.965 5.202 14DOPC C44 798 1.261 1.897 5.146 14DOPC C45 799 1.314 1.786 5.232 14DOPC C46 800 1.319 1.658 5.194 14DOPC C47 801 1.274 1.602 5.062 14DOPC C48 802 1.316 1.457 5.038 14DOPC C49 803 1.266 1.407 4.902 14DOPC C50 804 1.338 1.469 4.782 14DOPC C51 805 1.307 1.406 4.646 14DOPC C52 806 1.160 1.394 4.607 14DOPC C53 807 1.119 1.442 4.468 14DOPC C54 808 0.980 1.407 4.414 - after: - 14DOPCC1 755 0.136 1.777 6.423 14DOPCC2 756 0.279 1.580 6.384 14DOPCC3 757 0.383 1.799 6.403 14DOPCN4 758 0.260 1.726 6.354 14DOPCC5 759 0.263 1.741 6.204 14DOPCC6 760 0.386 1.685 6.132 14DOPC OS7 761 0.511 1.755 6.145 14DOPCP8 762 0.628 1.683 6.064 14DOPC OM9 763 0.640 1.548 6.123 14DOPC OM10 764 0.747 1.771 6.072 14DOPC OS11 765 0.576 1.681 5.913 14DOPC C12 766 0.591 1.806 5.845 14DOPC C13 767 0.470 1.901 5.846 14DOPC OS14 768 0.364 1.830 5.782 14DOPC C15 769 0.247 1.869 5.833 14DOPC O16 770 0.238 1.946 5.927 14DOPC C17 771 0.123 1.815 5.762 14DOPC C18 772 -0.004 1.897 5.786 14DOPC C19 773 -0.138 1.837 5.744 14DOPC C20 774 -0.147 1.817 5.593 14DOPC C21 775 -0.196 1.678 5.552 14DOPC C22 776 -0.181 1.637 5.406 14DOPC C23 777 -0.252 1.722 5.301 14DOPC C24 778 -0.241 1.664 5.163 14DOPC C25 779 -0.267 1.738 5.054 14DOPC C26 780 -0.312 1.881 5.044 14DOPC C27 781 -0.368 1.918 4.907 14DOPC C28 782 -0.266 1.941 4.795 14DOPC C29 783 -0.324 2.015 4.674 14DOPC C30 784 -0.377 1.920 4.567 14DOPC C31 785 -0.377 1.984 4.428 14DOPC C32 786 -0.439 1.894 4.321 14DOPC C33 787 -0.358 1.890 4.191 14DOPC C34 788 0.490 2.037 5.777 14DOPC OS35 789 0.541 2.029 5.644 14DOPC C36 790 0.591 2.142 5.593 14DOPC O37 791 0.595 2.252 5.646 14DOPC C38 792 0.674 2.092 5.476 14DOPC C39 793 0.818 2.145 5.475 14DOPC C40 794 0.906 2.056 5.387 14DOPC C41 795 1.042 2.123 5.364 14DOPC C42 796 1.160 2.029 5.339 14DOPC C43 797 1.136 1.965 5.202 14DOPC C44 798 1.261 1.897 5.146 14DOPC C45 799 1.314 1.786 5.232 14DOPC C46 800 1.319 1.658 5.194 14DOPC C47 801 1.274 1.602 5.062 14DOPC C48 802 1.316 1.457 5.038
Re: [gmx-users] MPI runs on a local computer
On Thu, Sep 19, 2013 at 2:48 PM, Xu, Jianqing x...@medimmune.com wrote: Dear all, I am learning the parallelization issues from the instructions on Gromacs website. I guess I got a rough understanding of MPI, thread-MPI, OpenMP. But I hope to get some advice about a correct way to run jobs. Say I have a local desktop having 16 cores. If I just want to run jobs on one computer or a single node (but multiple cores), I understand that I don't have to install and use OpenMPI, as Gromacs has its own thread-MPI included already and it should be good enough to run jobs on one machine. However, for some reasons, OpenMPI has already been installed on my machine, and I compiled Gromacs with it by using the flag: -DGMX_MPI=ON. My questions are: 1. Can I still use this executable (mdrun_mpi, built with OpenMPI library) to run multi-core jobs on my local desktop? Yes Or the default Thread-MPI is actually a better option for a single computer or single node (but multi-cores) for whatever reasons? Yes - lower overhead. 2. Assuming I can still use this executable, let's say I want to use half of the cores (8 cores) on my machine to run a job, mpirun -np 8 mdrun_mpi -v -deffnm md a). Since I am not using all the cores, do I still need to lock the physical cores to use for better performance? Something like -nt for Thread-MPI? Or it is not necessary? You will see improved performance if you set the thread affinity. There is no advantage in allowing the threads to move. b). For running jobs on a local desktop, or single node having ... say 16 cores, or even 64 cores, should I turn off the separate PME nodes (-npme 0)? Or it is better to leave as is? Depends, but usually best to use separate PME nodes. Try g_tune_pme, as Carsten suggests. 3. If I want to run two different projects on my local desktop, say one project takes 8 cores, the other takes 4 cores (assuming I have enough memory), I just submit the jobs twice on my desktop: nohup mpirun -np 8 mdrun_mpi -v -deffnm md1 log1 nohup mpirun -np 4 mdrun_mpi -v -deffnm md2 log2 Will this be acceptable ? Will two jobs be competing the resource and eventually affect the performance? Depends how many cores you have. If you want to share a node between mdruns, you should specify how many (real- or thread-) MPI ranks for each run, and how many OpenMP threads per rank, arrange for one thread per core, and use mdrun -pin and mdrun -pinoffset suitably. You should expect near linear scaling of each job when you are doing it right - but learn the behaviour of running one job per node first! Mark Sorry for so many detailed questions, but your help on this will be highly appreciated! Thanks a lot, Jianqing To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: grompp for minimization: note warning
The UNIX tool diff is your friend for comparing files. On Fri, Sep 20, 2013 at 1:53 PM, shahab shariati shahab.shari...@gmail.com wrote: Dear Tsjerk Thanks for your reply Before correcting the gro file, I knew that gro file is fixed format. I did this correction very carefully. Part of the gro file before and after correction is as follows: - before: - 14DOPCN4 755 0.260 1.726 6.354 14DOPCC5 756 0.263 1.741 6.204 14DOPCC1 757 0.136 1.777 6.423 14DOPCC2 758 0.279 1.580 6.384 14DOPCC3 759 0.383 1.799 6.403 14DOPCC6 760 0.386 1.685 6.132 14DOPCP8 761 0.628 1.683 6.064 14DOPC OM9 762 0.640 1.548 6.123 14DOPC OM10 763 0.747 1.771 6.072 14DOPC OS7 764 0.511 1.755 6.145 14DOPC OS11 765 0.576 1.681 5.913 14DOPC C12 766 0.591 1.806 5.845 14DOPC C13 767 0.470 1.901 5.846 14DOPC OS14 768 0.364 1.830 5.782 14DOPC C15 769 0.247 1.869 5.833 14DOPC O16 770 0.238 1.946 5.927 14DOPC C17 771 0.123 1.815 5.762 14DOPC C34 772 0.490 2.037 5.777 14DOPC OS35 773 0.541 2.029 5.644 14DOPC C36 774 0.591 2.142 5.593 14DOPC O37 775 0.595 2.252 5.646 14DOPC C38 776 0.674 2.092 5.476 14DOPC C18 777 -0.004 1.897 5.786 14DOPC C19 778 -0.138 1.837 5.744 14DOPC C20 779 -0.147 1.817 5.593 14DOPC C21 780 -0.196 1.678 5.552 14DOPC C22 781 -0.181 1.637 5.406 14DOPC C23 782 -0.252 1.722 5.301 14DOPC C24 783 -0.241 1.664 5.163 14DOPC C25 784 -0.267 1.738 5.054 14DOPC C26 785 -0.312 1.881 5.044 14DOPC C27 786 -0.368 1.918 4.907 14DOPC C28 787 -0.266 1.941 4.795 14DOPC C29 788 -0.324 2.015 4.674 14DOPC C30 789 -0.377 1.920 4.567 14DOPC C31 790 -0.377 1.984 4.428 14DOPC C32 791 -0.439 1.894 4.321 14DOPC C33 792 -0.358 1.890 4.191 14DOPC C39 793 0.818 2.145 5.475 14DOPC C40 794 0.906 2.056 5.387 14DOPC C41 795 1.042 2.123 5.364 14DOPC C42 796 1.160 2.029 5.339 14DOPC C43 797 1.136 1.965 5.202 14DOPC C44 798 1.261 1.897 5.146 14DOPC C45 799 1.314 1.786 5.232 14DOPC C46 800 1.319 1.658 5.194 14DOPC C47 801 1.274 1.602 5.062 14DOPC C48 802 1.316 1.457 5.038 14DOPC C49 803 1.266 1.407 4.902 14DOPC C50 804 1.338 1.469 4.782 14DOPC C51 805 1.307 1.406 4.646 14DOPC C52 806 1.160 1.394 4.607 14DOPC C53 807 1.119 1.442 4.468 14DOPC C54 808 0.980 1.407 4.414 - after: - 14DOPCC1 755 0.136 1.777 6.423 14DOPCC2 756 0.279 1.580 6.384 14DOPCC3 757 0.383 1.799 6.403 14DOPCN4 758 0.260 1.726 6.354 14DOPCC5 759 0.263 1.741 6.204 14DOPCC6 760 0.386 1.685 6.132 14DOPC OS7 761 0.511 1.755 6.145 14DOPCP8 762 0.628 1.683 6.064 14DOPC OM9 763 0.640 1.548 6.123 14DOPC OM10 764 0.747 1.771 6.072 14DOPC OS11 765 0.576 1.681 5.913 14DOPC C12 766 0.591 1.806 5.845 14DOPC C13 767 0.470 1.901 5.846 14DOPC OS14 768 0.364 1.830 5.782 14DOPC C15 769 0.247 1.869 5.833 14DOPC O16 770 0.238 1.946 5.927 14DOPC C17 771 0.123 1.815 5.762 14DOPC C18 772 -0.004 1.897 5.786 14DOPC C19 773 -0.138 1.837 5.744 14DOPC C20 774 -0.147 1.817 5.593 14DOPC C21 775 -0.196 1.678 5.552 14DOPC C22 776 -0.181 1.637 5.406 14DOPC C23 777 -0.252 1.722 5.301 14DOPC C24 778 -0.241 1.664 5.163 14DOPC C25 779 -0.267 1.738 5.054 14DOPC C26 780 -0.312 1.881 5.044 14DOPC C27 781 -0.368 1.918 4.907 14DOPC C28 782 -0.266 1.941 4.795 14DOPC C29 783 -0.324 2.015 4.674 14DOPC C30 784 -0.377 1.920 4.567 14DOPC C31 785 -0.377 1.984 4.428 14DOPC C32 786 -0.439 1.894 4.321 14DOPC C33 787 -0.358 1.890 4.191 14DOPC C34 788 0.490 2.037 5.777 14DOPC OS35 789 0.541 2.029 5.644 14DOPC C36 790 0.591 2.142 5.593 14DOPC O37 791 0.595 2.252 5.646 14DOPC C38 792 0.674 2.092 5.476 14DOPC C39 793 0.818 2.145 5.475 14DOPC C40 794 0.906 2.056 5.387 14DOPC C41 795 1.042 2.123 5.364 14DOPC C42 796 1.160 2.029 5.339 14DOPC C43 797
Re: [gmx-users] Re: Charmm 36 forcefield with verlet cut-off scheme
Note that the group scheme does not reproduce the (AFAIK unpublished) CHARMM switching scheme, either. Mark On Fri, Sep 20, 2013 at 4:26 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/19/13 9:55 PM, akk5r wrote: Thanks Justin. I was told that the vdwtype = switch was an essential component of running Charmm36. Is that not the case? It is, but I suppose one can achieve a similar effect with the Verlet scheme. You can certainly use the traditional CHARMM settings if you use the group scheme, instead. The vdw-modifier setting should give you a comparable result, but I have never tried it myself. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_covar average.pdb calculation
Dear All, I would like to get information on how g_covar calculates the average structure file (average.pdb) My aim was actually to get a covariance matrix (deltaR*deltaR) so I started off by writing my own code, I use MDAnalysis package, so I give psf and traj files as an input and I generate the coordinates for each frame, and if I have 3 frames, I take the average of each coordinate element for 3 frames. So for the 1st CA atom, I have x, y, z values for 3 frames. So I add x1, x2, x3 values and divide by the number of frames. So this gives me the average x coordinate of the 1st CA atom. I do the same for y and z and then for all CA atoms. So if x1, x2, x3 for CA1 is 49.5 49.0 and 49.4 for 3 frames, the average x i get is 49.3. This is what I call an average structure. After doing this, I wanted to compare this with what g_covar gives me (average.pdb) but found out that the result that I get from my own calculations and the result I get from g_covar are very very different. The g_covar command that I use is the following: g_covar -f traj.xtc -s topol.tpr -ascii covar.dat -xpm covar.xpm -noref Here I use -noref because I already use trjconv on my initial trajectory to generate a new trajectory so I do -pbc mol and center and -fit rot+trans to remove translation, rotation and to fit the structure. So I thought I could use -nofit in g_covar to not to fit to the reference structure again. So, coming back to my question, why would g_covar give me a very different result than what I find with my simple code? What does g_covar do to calculate this average structure? I thought maybe it does some fitting or additional stuff to what I'm doing in my code or changes the units, that in the end it doesn't give me the same coordinates for the average.pdb. - Deniz Aydin, BSc. Graduate Student Chemical Biological Engineering Graduate School of Sciences and Engineering Koç University, Istanbul, Turkey -- View this message in context: http://gromacs.5086.x6.nabble.com/g-covar-average-pdb-calculation-tp5011339.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_covar average.pdb calculation
Hi Deniz, The option -ref/-noref is not what you think it is. You want to use -nofit. Cheers, Tsjerk On Fri, Sep 20, 2013 at 2:26 PM, Deniz Aydin denizay...@ku.edu.tr wrote: Dear All, I would like to get information on how g_covar calculates the average structure file (average.pdb) My aim was actually to get a covariance matrix (deltaR*deltaR) so I started off by writing my own code, I use MDAnalysis package, so I give psf and traj files as an input and I generate the coordinates for each frame, and if I have 3 frames, I take the average of each coordinate element for 3 frames. So for the 1st CA atom, I have x, y, z values for 3 frames. So I add x1, x2, x3 values and divide by the number of frames. So this gives me the average x coordinate of the 1st CA atom. I do the same for y and z and then for all CA atoms. So if x1, x2, x3 for CA1 is 49.5 49.0 and 49.4 for 3 frames, the average x i get is 49.3. This is what I call an average structure. After doing this, I wanted to compare this with what g_covar gives me (average.pdb) but found out that the result that I get from my own calculations and the result I get from g_covar are very very different. The g_covar command that I use is the following: g_covar -f traj.xtc -s topol.tpr -ascii covar.dat -xpm covar.xpm -noref Here I use -noref because I already use trjconv on my initial trajectory to generate a new trajectory so I do -pbc mol and center and -fit rot+trans to remove translation, rotation and to fit the structure. So I thought I could use -nofit in g_covar to not to fit to the reference structure again. So, coming back to my question, why would g_covar give me a very different result than what I find with my simple code? What does g_covar do to calculate this average structure? I thought maybe it does some fitting or additional stuff to what I'm doing in my code or changes the units, that in the end it doesn't give me the same coordinates for the average.pdb. - Deniz Aydin, BSc. Graduate Student Chemical Biological Engineering Graduate School of Sciences and Engineering Koç University, Istanbul, Turkey -- View this message in context: http://gromacs.5086.x6.nabble.com/g-covar-average-pdb-calculation-tp5011339.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Significant slowdown in 4.6? (4.6.3)
I have a Intel i7-2630QM CPU @ 2.00GHz on my laptop with 4.6.3 installed and a desktop with an i3-3220 with 4.5.5 installed. I am trying the same energy minimization on each of these machines. My desktop takes a few seconds, my laptop takes hours. This doesn't make much sense bc benchmarks indicated that my laptop should be faster. Only conclusion I can come up with is that it is the difference in versions. Any other explanations? Here are the files I am using: http://www.sendspace.com/file/a1cdch List of commands used are found in: commands.txt I use the last command mdrun -v -deffnm em on each machine, and the files were built with 4.6.3 (my laptop). If you need any more information please let me know. Thank you! -Jonathan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: Significant slowdown in 4.6? (4.6.3)
Figured out the problem. For some reason one thread is being taken up 90% by the system. If I run it with 6 threads it runs fast. Never experienced this on linux though, very curious. Sorry if i wasted your time. -Jonathan Saboury On Fri, Sep 20, 2013 at 7:58 AM, Jonathan Saboury jsab...@gmail.com wrote: I have a Intel i7-2630QM CPU @ 2.00GHz on my laptop with 4.6.3 installed and a desktop with an i3-3220 with 4.5.5 installed. I am trying the same energy minimization on each of these machines. My desktop takes a few seconds, my laptop takes hours. This doesn't make much sense bc benchmarks indicated that my laptop should be faster. Only conclusion I can come up with is that it is the difference in versions. Any other explanations? Here are the files I am using: http://www.sendspace.com/file/a1cdch List of commands used are found in: commands.txt I use the last command mdrun -v -deffnm em on each machine, and the files were built with 4.6.3 (my laptop). If you need any more information please let me know. Thank you! -Jonathan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Minimum distance periodic images, protein simulation
Hello, I ran a 100-ns long simulation of a small protein (trp-cage) at an elevated temperature. I analysed the distance between periodic images using g_mindist -f md-run-1-noPBC.xtc -s md-run-1.tpr -n index.ndx -od mindist.xvg -pi The output shows that there are situations when the closest distance between certain atoms is much lesser than 1 nm. Conventional wisdom says that if this happens the simulation results are questionable. Is this completely true? If this is indeed true, how would I ensure that this does not happen again? I have posted the output of g_mindist at http://postimg.org/image/bnc0ej3nb/ Any comments and clarifications are highly appreciated Thanks, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Broken lipid molecules
HI, At the end of a MD run, the lipid molecules in a membrane protein are broken. I load .gro and .trr file into VMD to watch MD simulations, the lipids are broken at periodic boundaries. I try to fix it by trjconv -pbc nojump but output came with only 2 frames but initially it was 1500 frames. How to fix whole MD trajectory? Thanks Rama -- View this message in context: http://gromacs.5086.x6.nabble.com/Broken-lipid-molecules-tp5011344.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Broken lipid molecules
On 9/20/13 5:21 PM, Rama wrote: HI, At the end of a MD run, the lipid molecules in a membrane protein are broken. I load .gro and .trr file into VMD to watch MD simulations, the lipids are broken at periodic boundaries. I try to fix it by trjconv -pbc nojump but output came with only 2 frames but initially it was 1500 frames. Either something is wrong with the trajectory or something is wrong with the command you gave. Based on the information at hand, no one can say. How to fix whole MD trajectory? trjconv -pbc mol -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Minimum distance periodic images, protein simulation
On 9/20/13 4:11 PM, Arun Sharma wrote: Hello, I ran a 100-ns long simulation of a small protein (trp-cage) at an elevated temperature. I analysed the distance between periodic images using g_mindist -f md-run-1-noPBC.xtc -s md-run-1.tpr -n index.ndx -od mindist.xvg -pi The output shows that there are situations when the closest distance between certain atoms is much lesser than 1 nm. Conventional wisdom says that if this happens the simulation results are questionable. Is this completely true? If this is indeed true, how would I ensure that this does not happen again? Using a sufficiently large box (minimum solute-box distance at least equal to the longest cutoff) is the general procedure. I have posted the output of g_mindist at http://postimg.org/image/bnc0ej3nb/ Some configurations definitely come very close, indicating several frames with spurious forces throughout the duration of the trajectory. I would be very suspicious of the results. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
