I second this, very strongly. I wrestled with GROMACS for literally
a week trying to figure out the PME bug, and would really have
appreciated being able to easily learn about it.
The best solution to this, in my mind, is a 3.3.1 release with known
bugs patched. If this is unlikely to happen soon, I think I'll make
my own unofficial one (perhaps with extra goodies such as the ported
AMBER force fields). Are there any other sources of information
about known bugs/patches other than bugzilla.gromacs.org and CVS?
--Tom
On Mar 29, 2006, at 11:32 AM, David Mobley wrote:
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
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_____________________________________________________________________
___
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
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