[gmx-users] Error: relative constraint deviation after LINCS
raja
raja_28 at fastmail.us
Thu Mar 30 09:45:59 CEST 2006
Dear Tom,
Its is really annoying, I really struggled lot to compile it
initially. Now I forgot what are all the flags I enabled and
diabled for each step of compilation error in cygwin.
Any way thanks !
B.Nataraj
On Thu, 30 Mar 2006 02:02:42 -0500, "Tom Joseph"
<tom-lists at jambon.ll.cx> said:
> 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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> >>>>
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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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--
raja
raja_28 at fastmail.us
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