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

[Florian Haberl]

hi,

On Wednesday 29 March 2006 05:28, raja wrote:
> Hi gmxs,
>       No reply yet for this posting, so I reposting the same
>       error...Please give me the direction.

as serveral times posted here on the mailing list: 

- Your starting structure should be more relaxed (do a better em) 
- Perhaps your mdp file has some wrong parameters.

Search the list for lincs warning for more possibilities:

http://www.gromacs.org/search/index.php?query=lincs+warning&max=20&result=normal&sort=score&idxname=gromacs_site&idxname=mailing_lists

> 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


Florian

-- 
-------------------------------------------------------------------------------
 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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