You can maybe do up to triplet or quadruplets - it talks about doing that for default Lennard-Jones. You can modify the python script to extra loops e.g. over k. A key point is probably also to keep all exclusions the same length. Again I don't know much about this but thought I'd try to be helpful.
> Thank you a lot for this. As it states in the manual > [ exclusions ] > 1 2 3 > 2 1 3 > 3 1 2 > > But this makes repeats so I tried: > [exclusions] > 1 2 3 4 5 > 2 3 4 5 > 3 4 5 > 4 5 > > Both not working and the simulation crashes. I think there is too much > data... > > Steven > > > On Fri, Dec 6, 2013 at 12:44 PM, <jkrie...@mrc-lmb.cam.ac.uk> wrote: > >> I may be completely wrong but I think each line should be a pair with no >> pair represented in reverse e.g. >> 1 2 >> 1 3 >> 2 3 >> 1 4 >> 2 4 >> 3 4 >> and so on. >> >> Here's a python script to do this for your 2516 atoms. Indentation is >> part >> of the code and the standard indentation is 4 presses of the spacebar. >> >> f = open('exclusions.txt') >> f.write('[ exclusions ]') >> for i in range(2516): >> for j in range(2516): >> f.write(str(i+1, j+1)) >> f.close() >> >> i+1 and j+1 are used because python starts counting at 0 and atoms are >> counted starting at 1. >> >> You can use standard command line editing tools such as cat to join this >> into a file with other sections. >> >> > I generated the [ exclusions ] so that the maximum characters >> correspond >> > to >> > 4000 - line break is made after this. So I generated the tpr file with >> > grompp and when running: >> > >> > Reading file md.tpr, VERSION 4.5.5 (single precision) >> > Starting 8 threads >> > Making 2D domain decomposition 4 x 2 x 1 >> > *** glibc detected *** mdrun: realloc(): invalid next size: >> > 0x00002b2d801eebd0 *** >> > ======= Backtrace: ========= >> > /lib64/libc.so.6[0x300f873b64] >> > /lib64/libc.so.6(realloc+0x102)[0x300f875c92] >> > >> /usr/local/gromacs-4.5.5/lib/libgmx.so.6(save_realloc+0x4d)[0x2b2d792dc04d] >> > >> /usr/local/gromacs-4.5.5/lib/libmd.so.6(dd_make_local_top+0x1252)[0x2b2d78fcce82] >> > >> /usr/local/gromacs-4.5.5/lib/libmd.so.6(dd_partition_system+0x183c)[0x2b2d78f4005c] >> > mdrun(do_md+0x771)[0x41cb61] >> > mdrun(mdrunner+0xa3d)[0x40ce4d] >> > mdrun[0x40dd96] >> > /usr/local/gromacs-4.5.5/lib/libgmx.so.6[0x2b2d794fa14e] >> > /lib64/libpthread.so.0[0x301080683d] >> > /lib64/libc.so.6(clone+0x6d)[0x300f8d526d] >> > ======= Memory map: ======== >> > 00400000-00432000 r-xp 00000000 00:1d 149136 >> > /rvol/cpse-apps/RHEL5-x86_64/gromacs-4.5.5/bin/mdrun >> > 00631000-00633000 rwxp 00031000 00:1d 149136 >> > /rvol/cpse-apps/RHEL5-x86_64/gromacs-4.5.5/bin/mdrun >> > 00633000-00634000 rwxp 00633000 00:00 0 >> > 1c12c000-1c3dc000 rwxp 1c12c000 00:00 0 >> > [heap] >> > 300f400000-300f41c000 r-xp 00000000 08:02 43548681 >> > /lib64/ld-2.5.so >> > 300f61c000-300f61d000 r-xp 0001c000 08:02 43548681 >> > /lib64/ld-2.5.so >> > 300f61d000-300f61e000 rwxp 0001d000 08:02 43548681 >> > /lib64/ld-2.5.so >> > 300f800000-300f94f000 r-xp 00000000 08:02 43548690 >> > /lib64/libc-2.5.so >> > 300f94f000-300fb4f000 ---p 0014f000 08:02 43548690 >> > /lib64/libc-2.5.so >> > 300fb4f000-300fb53000 r-xp 0014f000 08:02 43548690 >> > /lib64/libc-2.5.so >> > 300fb53000-300fb54000 rwxp 00153000 08:02 43548690 >> > /lib64/libc-2.5.so >> > 300fb54000-300fb59000 rwxp 300fb54000 00:00 0 >> > 300fc00000-300fc82000 r-xp 00000000 08:02 43549057 >> > /lib64/libm-2.5.so >> > 300fc82000-300fe81000 ---p 00082000 08:02 43549057 >> > /lib64/libm-2.5.so >> > 300fe81000-300fe82000 r-xp 00081000 08:02 43549057 >> > /lib64/libm-2.5.so >> > 300fe82000-300fe83000 rwxp 00082000 08:02 43549057 >> > /lib64/libm-2.5.so >> > 3010000000-3010002000 r-xp 00000000 08:02 43548960 >> > /lib64/libdl-2.5.so >> > 3010002000-3010202000 ---p 00002000 08:02 43548960 >> > /lib64/libdl-2.5.so >> > 3010202000-3010203000 r-xp 00002000 08:02 43548960 >> > /lib64/libdl-2.5.so >> > 3010203000-3010204000 rwxp 00003000 08:02 43548960 >> > /lib64/libdl-2.5.so >> > 3010400000-3010414000 r-xp 00000000 08:02 43548948 >> > /lib64/libz.so.1.2.3 >> > 3010414000-3010613000 ---p 00014000 08:02 43548948 >> > /lib64/libz.so.1.2.3 >> > 3010613000-3010614000 rwxp 00013000 08:02 43548948 >> > /lib64/libz.so.1.2.3 >> > 3010800000-3010816000 r-xp 00000000 08:02 43548875 >> > /lib64/libpthread-2.5.so >> > 3010816000-3010a16000 ---p 00016000 08:02 43548875 >> > /lib64/libpthread-2.5.so >> > 3010a16000-3010a17000 r-xp 00016000 08:02 43548875 >> > /lib64/libpthread-2.5.so >> > 3010a17000-3010a18000 rwxp 00017000 08:02 43548875 >> > /lib64/libpthread-2.5.so >> > 3010a18000-3010a1c000 rwxp 3010a18000 00:00 0 >> > 3018a00000-3018b34000 r-xp 00000000 08:02 28578909 >> > /usr/lib64/libxml2.so.2.6.26 >> > 3018b34000-3018d34000 ---p 00134000 08:02 28578909 >> > /usr/lib64/libxml2.so.2.6.26 >> > 3018d34000-3018d3d000 rwxp 00134000 08:02 28578909 >> > /usr/lib64/libxml2.so.2.6.26 >> > 3018d3d000-3018d3e000 rwxp 3018d3d000 00:00 0 >> > 301da00000-301da0d000 r-xp 00000000 08:02 43549037 >> > /lib64/libgcc_s-4.1.2-20080825.so.1 >> > 301da0d000-301dc0d000 ---p 0000d000 08:02 43549037 >> > /lib64/libgcc_s-4.1.2-20080825.so.1 >> > 301dc0d000-301dc0e000 rwxp 0000d000 08:02 43549037 >> > /lib64/libgcc_s-4.1.2-20080825.so.1 >> > 2b2d78bef000-2b2d78bf1000 rwxp 2b2d78bef000 00:00 0 >> > 2b2d78c0f000-2b2d78c10000 rwxp 2b2d78c0f000 00:00 0 >> > 2b2d78c10000-2b2d78c9e000 r-xp 00000000 00:1d 149134 >> > /rvol/cpse-apps/RHEL5-x86_64/gromacs-4.5.5/lib/libgmxpreprocess.so.6 >> > 2b2d78c9e000-2b2d78e9d000 ---p 0008e000 00:1d 149134 >> > /rvol/cpse-apps/RHEL5-x86_64/gromacs-4.5.5/lib/libgmxpreprocess.so.6 >> > 2b2d78e9d000-2b2d78e9f000 rwxp 0008d000 00:1d 149134 >> > /rvol/cpse-apps/RHEL5-x86_64/gromacs-4.5.5/lib/libgmxpreprocess.so.6 >> > 2b2d78e9f000-2b2d78ecb000 rwxp 2b2d78e9f000 00:00 0 >> > 2b2d78ecb000-2b2d7900b000 r-xp 00000000 00:1d 149131 >> > /rvol/cpse-apps/RHEL5-x86_64/gromacs-4.5.5/lib/libmd.so.6 >> > 2b2d7900b000-2b2d7920b000 ---p 00140000 00:1d 149131 >> > /rvol/cpse-apps/RHEL5-x86_64/gromacs-4.5.5/lib/libmd.so.6 >> > 2b2d7920b000-2b2d7920d000 rwxp 00140000 00:1d 149131 >> > /rvol/cpse-apps/RHEL5-x86_64/gromacs-4.5.5/lib/libmd.so.6 >> > 2b2d7920d000-2b2d79558000 r-xp 00000000 00:1d 149128 >> > /rvol/cpse-apps/RHEL5-x86_64/gromacs-4.5.5/lib/libgmx.so.6 >> > 2b2d79558000-2b2d79758000 ---p 0034b000 00:1d 149128 >> > /rvol/cpse-apps/RHEL5-x86_64/gromacs-4.5.5/lib/libgmx.so.6 >> > 2b2d79758000-2b2d79768000 rwxp 0034b000 00:1d 149128 >> > /rvol/cpse-apps/RHEL5-x86_64/gromacs-4.5.5/lib/libgmx.so.6 >> > 2b2d79768000-2b2d7976a000 rwxp 2b2d79768000 00:00 0 >> > 2b2d7976a000-2b2d79865000 r-xp 00000000 00:1d 144523 >> > /rvol/cpse-apps/RHEL5-x86_64/fftw-3.3.3/lib/libfftw3f.so.3.3.2 >> > 2b2d79865000-2b2d79a65000 ---p 000fb000 00:1d 144523 >> > /rvol/cpse-apps/RHEL5-x86_64/fftw-3.3.3/lib/libfftw3f.so.3.3.2 >> > 2b2d79a65000-2b2d79a6c000 rwxp 000fb000 00:1d 144523 >> > /rvol/cpse-apps/RHEL5-x86_64/fftw-3.3.3/lib/libfftw3f.so.3.3.2 >> > 2b2d79a6c000-2b2d79b6f000 rwxp 2b2d79a6c000 00:00 0 >> > 2b2d79c6f000-2b2d7b495000 rwxp 2b2d79c6f000 00:00 0 >> > 2b2d7b495000-2b2d7b496000 ---p 2b2d7b495000 00:00 0 >> > 2b2d7b496000-2b2d7b696000 rwxp 2b2d7b496000 00:00 0 >> > 2b2d7b696000-2b2d7b697000 ---p 2b2d7b696000 00:00 0 >> > 2b2d7b697000-2b2d7b897000 rwxp 2b2d7b697000 00:00 0 >> > 2b2d7b897000-2b2d7b898000 ---p 2b2d7b897000 00:00 0 >> > 2b2d7b898000-2b2d7ba98000 rwxp 2b2d7b898000 00:00 0 >> > 2b2d7ba98000-2b2d7ba99000 ---p 2b2d7ba98000 00:00 0 >> > 2b2d7ba99000-2b2d7bc99000 rwxp 2b2d7ba99000 00:00 0 >> > 2b2d7c000000-2b2d7c1d8000 rwxp 2b2d7c000000 00:00 0 >> > 2b2d7c1d8000-2b2d80000000 ---p 2b2d7c1d8000 00:00 0 >> > 2b2d80000000-2b2d801f6000 rwxp 2b2d80000000 00:00 0 >> > 2b2d801f6000-2b2d84000000 ---p 2b2d801f6000 00:00 0 >> > 2b2d84000000-2b2d84001000 ---p 2b2d84000000 00:00 0 >> > 2b2d84001000-2b2d84201000 rwxp 2b2d84001000 00:00 0 >> > 2b2d84201000-2b2d84202000 ---p 2b2d84201000 00:00 0 >> > 2b2d84202000-2b2d84402000 rwxp 2b2d84202000 00:00 0 >> > 2b2d84402000-2b2d84403000 ---p 2b2d84402000 00:00 0 >> > 2b2d84403000-2b2d84603000 rwxp 2b2d84403000 00:00 0 >> > 2b2d88000000-2b2d88219000 rwxp 2b2d88000000 00:00 0 >> > 2b2d88219000-2b2d8c000000 ---p 2b2d88219000 00:00 0 >> > 2b2d8c000000-2b2d8c1c0000 rwxp 2b2d8c000000 00:00 0 >> > 2b2d8c1c0000-2b2d90000000 ---p 2b2d8c1c0000 00:00 0 >> > 2b2d90000000-2b2d901ea000 rwxp 2b2d90000000 00:00 0 >> > 2b2d901ea000-2b2d94000000 ---p 2b2d901ea000 00:00 0 >> > 2b2d94000000-2b2d941bd000 rwxp 2b2d94000000 00:00 0 >> > 2b2d941bd000-2b2d98000000 ---p 2b2d941bd000 00:00 0 >> > 2b2d98000000-2b2d9816a000 rwxp 2b2d98000000 00:00 0 >> > 2b2d9816a000-2b2d9c000000 ---p 2b2d9816a000 00:00 0 >> > 2b2d9c000000-2b2da6a26000 rwxp 2b2d9c000000 00:00 0 >> > 2b2da6a98000-2b2da6b26000 rwxp 2b2da6a98000 00:00 0 >> > 2b2da6bdf000-2b2da6cb4000 rwxp 2b2da6bdf000 00:00 0 >> > 2b2da6d6d000-2b2da6ed0000 rwxp 2b2da6d6d000 00:00 0 >> > 2b2da6f0a000-2b2da7217000 rwxp 2b2da6f0a000 00:00 0 >> > 2b2da7242000-2b2da76f9000 rwxp 2b2da7242000 00:00 0 >> > 2b2da7708000-2b2da7987000 rwxp 2b2da7708000 00:00 0 >> > 2b2da7a40000-2b2da7b5c000 rwxp 2b2da7a40000 00:00 0 >> > 2b2da7c40000-2b2da82a1000 rwxp 2b2da7c40000 00:00 0 >> > 2b2da82bf000-2b2da8613000 rwxp 2b2da82bf000 00:00 0 >> > 2b2da8622000-2b2da8b67000 rwxp 2b2da8622000 00:00 0 >> > 2b2da8b92000-2b2da900d000 rwxp 2b2da8b92000 00:00 0 >> > 2b2da9025000-2b2da907a000 rwxp 2b2da9005000 00:00 0 >> > 2b2da910c000-2b2da9167000 rwxp 2b2da8fd2000 00:00 0 >> > 7fffade95000-7fffadea7000 rwxp 7ffffffe9000 00:00 0 >> > [stack] >> > 7fffadea7000-7fffadeaa000 rw-p 7fffffffc000 00:00 0 >> > 7fffadffd000-7fffae000000 r-xp 7fffadffd000 00:00 0 >> > [vdso] >> > ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 >> > [vsyscall] >> > Abort >> > >> > >> > simulation is aborted. Would you please advise? >> > >> > Steven >> > >> > >> > On Fri, Dec 6, 2013 at 9:39 AM, Steven Neumann >> > <s.neuman...@gmail.com>wrote: >> > >> >> I used bonds but with [ exclusions ] of 2516 atoms: >> >> 1 2 3..... 2516 >> >> 2 3 4 .....2516 >> >> ... >> >> 2515 2516 >> >> >> >> when grompp I get an error: >> >> >> >> "An input file contains a line longer than 4095 characters". It does >> >> indeed contains over 4095 as its 11470. Do you know how to overcome >> >> this? >> >> >> >> Steven >> >> >> >> >> >> >> >> On Thu, Dec 5, 2013 at 7:25 PM, Steven Neumann >> >> <s.neuman...@gmail.com>wrote: >> >> >> >>> Thank you! >> >>> >> >>> Steven >> >>> >> >>> >> >>> On Thu, Dec 5, 2013 at 6:03 PM, Justin Lemkul <jalem...@vt.edu> >> wrote: >> >>> >> >>>> >> >>>> >> >>>> On 12/5/13 12:57 PM, Steven Neumann wrote: >> >>>> >> >>>>> Thanks, I will apply harmonic bonds with whatever force constant >> >>>>> then. >> >>>>> Would that speed up the performance with all exclusions and bonds? >> >>>>> >> >>>> >> >>>> Exclusions would make a big difference. Bonds will not produce any >> >>>> noticeable change. >> >>>> >> >>>> >> >>>> Does the increase of the force constant in posre.itp make the >> >>>> simulation >> >>>>> slower? I used Fx=Fy=Fz=30 000 >> >>>>> >> >>>>> >> >>>> No. >> >>>> >> >>>> >> >>>> -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 >> >>>> >> >>>> ================================================== >> >>>> -- >> >>>> 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. >> > -- > 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.