[gmx-users] Error: relative constraint deviation after LINCS
David van der Spoel
spoel at xray.bmc.uu.se
Wed Mar 29 14:56:39 CEST 2006
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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