[gmx-users] Error: relative constraint deviation after LINCS
David Mobley
dmobley at gmail.com
Wed Mar 29 18:32:54 CEST 2006
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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