Hi, So many posts and replies on a single issue, and still no exact command lines, nor grompp output, nor gromacs version. Lin, please be aware that such errors only make sense in the context of what you did. You'll have to provide all information that might be related to it. I'm pretty sure that your command lines will reveal the problem, and otherwise the grompp output will.
If I have to make a guess, which is all one can do with the information provided, I'd say the PBC is incorrect. Maybe you converted to .pdb format at an intermediary step which is known to remove the PBC in some gromacs versions. Cheers, Tsjerk On Thu, Dec 31, 2009 at 2:47 AM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > Chih-Ying Lin wrote: >> >> Hi >> what does the max max 597108032.000000 (between atoms 366 and 368) mean? >> is it the max force or max length of the system? >> where is the max force listed? > > Don't know. > >> max 597108032.000000 (between atoms 366 and 368) rms 26394490.000000 >> bonds that rotated more than 30 degrees: >> what does previous, current mean? >> is it previous length and current length? > > Yeah probably. You need to understand what LINCS does to make some sense of > this output. > > It doesn't really matter though. A well-behaved simulation will have none of > these warnings. Atoms 366 and 368 are connected by a constraint and unhappy > at the start of the simulation. In the output you quote, their distance has > gone from under 1nm to a ridiculous number. Look at the region of those > atoms in the starting configuration, and work out why. The most likely > hypothesis is that some other atom is so close to them that they experienced > a massive force, and had massive LJ. > > Mark > >> Thank you >> Lin >> Step 0, time 0 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> max 597108032.000000 (between atoms 366 and 368) rms 26394490.000000 >> bonds that rotated more than 30 degrees: >> *atom 1 atom 2 angle previous, current, constraint length >> * 26 39 52.0 0.1530 0.1699 0.1530 39 40 69.4 >> 0.1230 0.1423 0.1230 39 41 40.7 0.1330 0.1502 >> 0.1330 75 76 36.0 0.1250 0.1252 0.1250 133 >> 134 69.5 0.1530 0.1937 0.1530 >> 134 135 89.8 0.1470 0.2036 0.1470 >> 344 346 42.4 0.1470 0.2090 0.1470 >> 346 347 42.2 0.1530 0.2141 0.1530 >> 346 359 63.9 0.1530 26006.0332 0.1530 >> 359 360 56.9 0.1230 26006.0469 0.1230 >> 359 361 83.2 0.1330 82898.5859 0.1330 >> 361 362 77.5 0.1000 82845.7109 0.1000 >> 361 363 83.8 0.1470 398710.1875 0.1470 >> 363 364 89.3 0.1530 1909291.8750 0.1530 >> 363 369 85.2 0.1530 393002.8125 0.1530 >> 364 365 90.0 0.1508 31146174.0000 0.1530 >> 365 366 90.2 0.1544 66925512.0000 0.1530 >> 366 367 92.7 0.1301 73689816.0000 0.1250 >> 366 368 87.0 0.1305 74638504.0000 0.1250 >> 369 370 72.1 0.1230 65978.3203 0.1230 >> 369 371 72.6 0.1330 66864.2812 0.1330 >> 371 372 85.7 0.1000 10685.0596 0.1000 >> 371 373 61.0 0.1470 10685.1035 0.1470 373 374 >> 33.3 0.1530 0.1896 0.1530 >> 373 377 33.5 0.1530 0.1933 0.1530 >> 547 548 90.1 0.1089 0.1358 0.1090 >> 898 900 89.9 0.1530 0.4741 0.1530 >> > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
