[gmx-users] exclusions

jkrieger at mrc-lmb.cam.ac.uk jkrieger at mrc-lmb.cam.ac.uk
Fri Dec 6 16:05:41 CET 2013 

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, <jkrieger at 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.neumann08 at 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.neumann08 at gmail.com>wrote:
>> >>
>> >>> Thank you!
>> >>>
>> >>> Steven
>> >>>
>> >>>
>> >>> On Thu, Dec 5, 2013 at 6:03 PM, Justin Lemkul <jalemkul at 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
>> >>>>
>> >>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> >>>>
>> >>>> ==================================================
>> >>>> --
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>> >>>
>> >>>
>> >>
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