[gmx-users] Error: relative constraint deviation after LINCS
Tom Joseph
tom-lists at jambon.ll.cx
Thu Mar 30 09:02:42 CEST 2006
Sorry, but the right way to do it is to recompile GROMACS. Annoying,
yes, but necessary :)
--Tom
On Mar 30, 2006, at 1:55 AM, raja wrote:
> Dear all,
> Thanks for your thoughts and suggestions. Please tell me how to update
> that patch,pme.c in already
> installed gromacs program. I mean to ask you whether I have to compile
> the gromacs again or is there easy way of adding pme.c patch file
> without recomipiling entire program.
>
> With thanks!
> B.Nataraj
>
>
>
>
>
>
>
> On Wed, 29 Mar 2006 08:32:54 -0800, "David Mobley" <dmobley at gmail.com>
> said:
>> 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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>>>
>>> --
>>> 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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> --
> raja
> raja_28 at fastmail.us
>
> --
> http://www.fastmail.fm - Does exactly what it says on the tin
>
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