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" <[EMAIL PROTECTED]> 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" <[EMAIL PROTECTED]> > > 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 <[EMAIL PROTECTED]> 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 > >>>>> [EMAIL PROTECTED] > >>>>> > >>>>> --http://www.fastmail.fm - The way an email service should be > >>>>> > >>>>> _______________________________________________ > >>>>> gmx-users mailing list gmx-users@gromacs.org > >>>>> http://www.gromacs.org/mailman/listinfo/gmx-users > >>>>> Please don't post (un)subscribe requests to the list. Use the > >>>>> www interface or send it to [EMAIL PROTECTED] > >>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >>>> > >>>> _______________________________________________ > >>>> gmx-users mailing list gmx-users@gromacs.org > >>>> http://www.gromacs.org/mailman/listinfo/gmx-users > >>>> Please don't post (un)subscribe requests to the list. Use thewww > >>>> interface or send it to [EMAIL PROTECTED] > >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >>> > >>> > >>> -- > >>> 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 > >>> [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > >>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > >>> ++++++ > >>> _______________________________________________ > >>> gmx-users mailing list gmx-users@gromacs.org > >>> http://www.gromacs.org/mailman/listinfo/gmx-users > >>> Please don't post (un)subscribe requests to the list. Use the > >>> www interface or send it to [EMAIL PROTECTED] > >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >>> > >> _______________________________________________ > >> gmx-users mailing list gmx-users@gromacs.org > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to [EMAIL PROTECTED] > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > > raja > > [EMAIL PROTECTED] > > > > -- > > http://www.fastmail.fm - Does exactly what it says on the tin > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - The way an email service should be _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php