Re: [gmx-users] LINCS WARNING max 597108032.000000 (between atoms 366 and 368) ?
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 597108032.00 (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 597108032.00 (between atoms 366 and 368) rms 26394490.00 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 597108032.00 (between atoms 366 and 368) rms 26394490.00 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. 0.1530 365 366 90.2 0.1544 66925512. 0.1530 366 367 92.7 0.1301 73689816. 0.1250 366 368 87.0 0.1305 74638504. 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 listgmx-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
[gmx-users] LINCS WARNING max 597108032.000000 (between atoms 366 and 368) ?
Hi what does the max max 597108032.00 (between atoms 366 and 368) mean? is it the max force or max length of the system? where is the max force listed? max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: what does previous, current mean? is it previous length and current length? Thank you Lin Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: *atom 1 atom 2 angle previous, current, constraint length * 26 39 52.00.1530 0.1699 0.1530 39 40 69.40.1230 0.1423 0.1230 39 41 40.70.1330 0.1502 0.1330 75 76 36.00.1250 0.1252 0.1250 133134 69.50.1530 0.1937 0.1530 134135 89.80.1470 0.2036 0.1470 344346 42.40.1470 0.2090 0.1470 346347 42.20.1530 0.2141 0.1530 346359 63.90.1530 26006.0332 0.1530 359360 56.90.1230 26006.0469 0.1230 359361 83.20.1330 82898.5859 0.1330 361362 77.50.1000 82845.7109 0.1000 361363 83.80.1470 398710.1875 0.1470 363364 89.30.1530 1909291.8750 0.1530 363369 85.20.1530 393002.8125 0.1530 364365 90.00.1508 31146174. 0.1530 365366 90.20.1544 66925512. 0.1530 366367 92.70.1301 73689816. 0.1250 366368 87.00.1305 74638504. 0.1250 369370 72.10.1230 65978.3203 0.1230 369371 72.60.1330 66864.2812 0.1330 371372 85.70.1000 10685.0596 0.1000 371373 61.00.1470 10685.1035 0.1470 373374 33.30.1530 0.1896 0.1530 373377 33.50.1530 0.1933 0.1530 547548 90.10.1089 0.1358 0.1090 898900 89.90.1530 0.4741 0.1530 -- gmx-users mailing listgmx-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
Re: [gmx-users] LINCS WARNING max 597108032.000000 (between atoms 366 and 368) ?
Chih-Ying Lin wrote: Hi what does the max max 597108032.00 (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 597108032.00 (between atoms 366 and 368) rms 26394490.00 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 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: *atom 1 atom 2 angle previous, current, constraint length * 26 39 52.00.1530 0.1699 0.1530 39 40 69.40.1230 0.1423 0.1230 39 41 40.70.1330 0.1502 0.1330 75 76 36.00.1250 0.1252 0.1250 133134 69.50.1530 0.1937 0.1530 134135 89.80.1470 0.2036 0.1470 344346 42.40.1470 0.2090 0.1470 346347 42.20.1530 0.2141 0.1530 346359 63.90.1530 26006.0332 0.1530 359360 56.90.1230 26006.0469 0.1230 359361 83.20.1330 82898.5859 0.1330 361362 77.50.1000 82845.7109 0.1000 361363 83.80.1470 398710.1875 0.1470 363364 89.30.1530 1909291.8750 0.1530 363369 85.20.1530 393002.8125 0.1530 364365 90.00.1508 31146174. 0.1530 365366 90.20.1544 66925512. 0.1530 366367 92.70.1301 73689816. 0.1250 366368 87.00.1305 74638504. 0.1250 369370 72.10.1230 65978.3203 0.1230 369371 72.60.1330 66864.2812 0.1330 371372 85.70.1000 10685.0596 0.1000 371373 61.00.1470 10685.1035 0.1470 373374 33.30.1530 0.1896 0.1530 373377 33.50.1530 0.1933 0.1530 547548 90.10.1089 0.1358 0.1090 898900 89.90.1530 0.4741 0.1530 -- gmx-users mailing listgmx-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
Re: [gmx-users] LINCS WARNING max 597108032.000000 (between atoms 366 and 368) ?
Chih-Ying Lin wrote: Hi what does the max max 597108032.00 (between atoms 366 and 368) mean? is it the max force or max length of the system? where is the max force listed? It corresponds to the length between the constrained atoms. Forces are printed to the .trr file if you have set nstfout 0. max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: what does previous, current mean? The constraint length at the previous step and the current one. Judging by the size of these values, it means your system is exploding hopelessly, as the constrained bond is currently at nearly infinite length. -Justin is it previous length and current length? Thank you Lin Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: *atom 1 atom 2 angle previous, current, constraint length * 26 39 52.00.1530 0.1699 0.1530 39 40 69.40.1230 0.1423 0.1230 39 41 40.70.1330 0.1502 0.1330 75 76 36.00.1250 0.1252 0.1250 133134 69.50.1530 0.1937 0.1530 134135 89.80.1470 0.2036 0.1470 344346 42.40.1470 0.2090 0.1470 346347 42.20.1530 0.2141 0.1530 346359 63.90.1530 26006.0332 0.1530 359360 56.90.1230 26006.0469 0.1230 359361 83.20.1330 82898.5859 0.1330 361362 77.50.1000 82845.7109 0.1000 361363 83.80.1470 398710.1875 0.1470 363364 89.30.1530 1909291.8750 0.1530 363369 85.20.1530 393002.8125 0.1530 364365 90.00.1508 31146174. 0.1530 365366 90.20.1544 66925512. 0.1530 366367 92.70.1301 73689816. 0.1250 366368 87.00.1305 74638504. 0.1250 369370 72.10.1230 65978.3203 0.1230 369371 72.60.1330 66864.2812 0.1330 371372 85.70.1000 10685.0596 0.1000 371373 61.00.1470 10685.1035 0.1470 373374 33.30.1530 0.1896 0.1530 373377 33.50.1530 0.1933 0.1530 547548 90.10.1089 0.1358 0.1090 898900 89.90.1530 0.4741 0.1530 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
