[gmx-users] exclusions

Justin Lemkul jalemkul at vt.edu
Fri Dec 6 20:26:05 CET 2013 


On 12/6/13 10:21 AM, Steven Neumann wrote:
> Thank you. Justin, would you please advise about this as well as the crash
> I got?
>

Sorry, no real insight aside from the fact that what you are doing is probably 
considered extremely abnormal relative to what the Gromacs algorithms expect, so 
it may be a bug related to an untested case.

-Justin

> Steven
>
>
> On Fri, Dec 6, 2013 at 3:05 PM, <jkrieger at mrc-lmb.cam.ac.uk> wrote:
>
>> 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
>>>>>>>>
>>>>>>>> ==================================================
>>>>>>>> --
>>>>>>>> Gromacs Users mailing list
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>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>> --
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-- 
==================================================

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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