[gmx-users] Error: relative constraint deviation after LINCS

Yang Ye leafyoung81-group at yahoo.com
Thu Mar 30 11:14:38 CEST 2006


you need to compile again.

Yang Ye

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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