[gmx-users] Error: relative constraint deviation after LINCS
David van der Spoel
spoel at xray.bmc.uu.se
Wed Mar 29 22:22:51 CEST 2006
Tom Joseph wrote:
> I second this, very strongly. I wrestled with GROMACS for literally a
> week trying to figure out the PME bug, and would really have
> appreciated being able to easily learn about it.
>
> The best solution to this, in my mind, is a 3.3.1 release with known
> bugs patched. If this is unlikely to happen soon, I think I'll make my
> own unofficial one (perhaps with extra goodies such as the ported AMBER
> force fields). Are there any other sources of information about known
> bugs/patches other than bugzilla.gromacs.org and CVS?
Tom,
you're welcome to help! Right now we're working our way through
bugzilla, and David M. is very helpful indeed by providing us with new
stuff to work on. We probably have to settle on a release soon, where
there at least are no known bugs in mdrun. Right now we have bugs 40,
49, 58 and 59 left. None of them is critical *for most users*. Some of
these probelms are obscure and hard to reproduce. They may be bugs in
gromacs or in the compiler. Although compilers have become better over
the years, we've had our fair share of bug reports (even due to bugs in
hardware) that make gromacs look suspicious.
Anyway, if you want to help you could try finding some nice example for
bug 58.
There is also a page on http://www.gromacs.org/features/changes33.html
showing documented fixes between 3.2 and 3.3 (not entirely complete, but
pretty good). This page will be made easier to find on the website
that's coming up *real soon now*.
>
> --Tom
>
> On Mar 29, 2006, at 11:32 AM, David Mobley wrote:
>
>> Regarding the PME bug, I know I've said this before, but I think it
>> would be a lot easier for people to find out about these things if
>> there were a single page somewhere on the site that lists all of the
>> known bugs with each version (and preferably their symptoms) and
>> possibly also links to fixes. If I were a new user and just
>> downloading 3.3 for the first time, I don't know how I would know that
>> there is a bug with PME without searching the archives of the mailing
>> list. Maybe even the 3.3 source available to download could be updated
>> with patches every so often? Again, I'm just a bit nervous that people
>> may be having problems due to *known bugs* in 3.3 simply because there
>> is no easy way to find out about these bugs or their solutions.
>>
>> David
>>
>> On 3/29/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>>
>>> Tom Joseph wrote:
>>>
>>>> Curiously, what is pme_order set to in your mdp file? I experienced a
>>>> very similar problem as you did when I had set pme_order to 6, and I
>>>> don't know why...
>>>
>>> it's a known bug, please fetch the new pme.c from the ftp site.
>>>
>>>>
>>>> --Tom
>>>>
>>>> On Mar 28, 2006, at 10:28 PM, raja wrote:
>>>>
>>>>> Hi gmxs,
>>>>> No reply yet for this posting, so I reposting the same
>>>>> error...Please give me the direction.
>>>>> With thanks !
>>>>> B.Nataraj
>>>>>
>>>>> The Error part
>>>>> ###################################################################
>>>>> #######################################
>>>>>
>>>>> step 0
>>>>> Step 10, time 0.02 (ps) LINCS WARNING
>>>>> relative constraint deviation after LINCS:
>>>>> max 0.002406 (between atoms 2664 and 2666) rms 0.000090
>>>>> bonds that rotated more than 30 degrees:
>>>>> atom 1 atom 2 angle previous, current, constraint length
>>>>> 2664 2665 31.5 0.1090 0.1091 0.1090
>>>>> step 30, will finish at Tue Mar 28 14:14:30 2006
>>>>> Step 38, time 0.076 (ps) LINCS WARNING
>>>>> relative constraint deviation after LINCS:
>>>>> max 0.296349 (between atoms 2576 and 2577) rms 0.004434
>>>>> bonds that rotated more than 30 degrees:
>>>>> atom 1 atom 2 angle previous, current, constraint length
>>>>> 2576 2577 90.0 0.1090 0.1413 0.1090
>>>>> 2578 2579 90.0 0.1090 0.1180 0.1090
>>>>>
>>>>> Step 39, time 0.078 (ps) LINCS WARNING
>>>>> relative constraint deviation after LINCS:
>>>>> max 4821.659668 (between atoms 2584 and 2585) rms 70.115692
>>>>> bonds that rotated more than 30 degrees:
>>>>> atom 1 atom 2 angle previous, current, constraint length
>>>>> 2557 2559 104.4 0.1450 0.5221 0.1449
>>>>> 2559 2560 87.2 0.1090 0.5446 0.1090
>>>>> 2559 2561 118.5 0.1530 0.5012 0.1529
>>>>> 2559 2572 99.8 0.1523 1.4141 0.1522
>>>>> 2561 2562 82.9 0.1090 0.0423 0.1090
>>>>> 2561 2563 69.9 0.1091 0.0341 0.1090
>>>>> 2561 2564 34.2 0.1529 0.0840 0.1529
>>>>> 2572 2573 88.1 0.1231 1.5691 0.1229
>>>>> 2572 2574 110.8 0.1335 6.8042 0.1335
>>>>> 2574 2575 106.0 0.1010 6.5640 0.1010
>>>>> 2574 2576 81.3 0.1456 8.8651 0.1449
>>>>> 2576 2577 41.1 0.1413 5.5404 0.1090
>>>>> 2576 2578 112.6 0.1532 12.6753 0.1529
>>>>> 2576 2588 100.3 0.1526 10.1017 0.1522
>>>>> 2578 2579 87.1 0.1180 54.2609 0.1090
>>>>> 2578 2580 92.4 0.1534 18.2981 0.1529
>>>>> 2578 2584 88.1 0.1538 35.5616 0.1529
>>>>> 2580 2581 89.1 0.1092 1.3620 0.1090
>>>>> 2580 2582 90.1 0.1090 1.4119 0.1090
>>>>> 2580 2583 88.1 0.1091 1.2295 0.1090
>>>>> 2584 2585 90.0 0.1090 525.6699 0.1090
>>>>> 2584 2586 91.5 0.1089 23.0823 0.1090
>>>>> 2584 2587 92.0 0.1089 22.9080 0.1090
>>>>> 2588 2589 104.3 0.1229 3.1250 0.1229
>>>>> 2588 2590 115.1 0.1335 2.8415 0.1335
>>>>> 2590 2591 109.1 0.1450 0.9337 0.1449
>>>>> 2590 2599 108.6 0.1450 0.9203 0.1449
>>>>> 2591 2592 112.4 0.1090 0.3062 0.1090
>>>>> 2591 2593 108.3 0.1529 0.2859 0.1529
>>>>> 2591 2602 120.1 0.1522 0.2576 0.1522
>>>>> 2593 2594 43.8 0.1090 0.1570 0.1090
>>>>> 2593 2595 45.3 0.1090 0.1562 0.1090
>>>>> 2596 2597 30.6 0.1090 0.1273 0.1090
>>>>> 2596 2598 41.2 0.1090 0.1451 0.1090
>>>>> 2596 2599 96.6 0.1529 0.1996 0.1529
>>>>> 2599 2600 133.4 0.1090 0.2447 0.1090
>>>>> 2599 2601 135.4 0.1090 0.2755 0.1090
>>>>> 2602 2603 32.1 0.1229 0.1593 0.1229
>>>>> 2602 2604 32.6 0.1335 0.1740 0.1335
>>>>> Segmentation fault (core dumped)
>>>>> ###################################################################
>>>>> ############################
>>>>>
>>>>> -- raja
>>>>> raja_28 at fastmail.us
>>>>>
>>>>> --http://www.fastmail.fm - The way an email service should be
>>>>>
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>>>>
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>>>
>>>
>>> --
>>> David.
>>> _____________________________________________________________________
>>> ___
>>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>>> Dept. of Cell and Molecular Biology, Uppsala University.
>>> Husargatan 3, Box 596, 75124 Uppsala, Sweden
>>> phone: 46 18 471 4205 fax: 46 18 511 755
>>> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>> +++++
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>
>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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