This [ molecules ] directive is at the end of the topology, right ? I was scared all my simulations went wrong. I have the correct order in molecules directive.
[ molecules ] SS1 1 SS2 1 Neutral 536 Positive 137 Negative 71 The particles in gro file are in this order. Thank you! On Tue, Nov 9, 2010 at 12:37 PM, Justin A. Lemkul <[email protected]> wrote: > > > Nimesh Jain wrote: > >> Hi, >> >> I was wondering if the order of molecules in topology file and the order >> of coordinates in gro file have to be same. My files are as follows: >> >> gro file: >> 1624 >> 1B1 C 1 22.237 30.408 26.522 >> 1B1 SA 2 22.348 30.033 26.829 >> 1B1 P 3 22.125 30.102 27.144 >> 2B2 T 4 21.852 30.069 26.468 >> 2B2 SA 5 21.824 30.189 26.949 >> 2B2 P 6 21.450 30.060 27.068 >> 3B3 G 7 21.778 29.762 26.361 >> 3B3 SA 8 21.321 30.008 26.724 >> 3B3 P 9 20.949 29.853 26.660 >> 4B4 G 10 21.629 29.470 26.321 >> 4B4 SA 11 21.026 29.716 26.325 >> 4B4 P 12 20.750 29.499 26.117 >> 5B5 A 13 21.487 29.154 26.338 >> 5B5 SA 14 20.990 29.299 25.943 >> 5B5 P 15 20.872 28.995 25.697 >> 6B6 G 16 21.351 28.838 26.366 >> 6B6 SA 17 21.165 28.798 25.747 >> 6B6 P 18 21.201 28.428 25.579 >> 7B7 A 19 21.229 28.513 26.410 >> 7B7 SA 20 21.416 28.303 25.825 >> 7B7 P 21 21.542 27.915 25.815 >> 8B8 T 22 21.195 28.076 26.416 >> 8B8 SA 23 21.574 27.883 26.158 >> 8B8 P 24 21.640 27.516 26.330 >> 9B9 A 25 20.912 27.888 26.523 >> 9B9 SA 26 21.488 27.595 26.632 >> ................................................... >> ................................................... upto 880 particles >> then, >> 295NEU NEU 881 27.530 28.268 24.349 >> 296NEU NEU 882 27.355 27.969 24.193 >> 297NEU NEU 883 27.623 27.876 23.941 >> 298NEU NEU 884 27.801 27.639 24.177 >> 299NEU NEU 885 27.473 27.507 24.322 >> 300NEU NEU 886 27.376 27.410 23.963 >> 301NEU NEU 887 27.316 26.930 24.121 >> 302NEU NEU 888 27.540 26.452 24.221 >> 303NEU NEU 889 27.266 26.353 23.979 >> 304NEU NEU 890 27.681 25.977 24.053 >> 305NEU NEU 891 27.538 25.708 24.281 >> ............................................................. upto 1416 >> particles then, >> 831POS POS 1417 27.764 28.400 24.075 >> 832POS POS 1418 27.717 27.250 23.909 >> 833POS POS 1419 27.466 26.805 23.792 >> 834POS POS 1420 27.758 26.635 23.970 >> 835POS POS 1421 27.530 26.183 23.770 >> 836POS POS 1422 27.930 25.982 25.593 >> 837POS POS 1423 27.940 25.614 25.687 >> 838POS POS 1424 27.629 25.568 26.499 >> 839POS POS 1425 27.293 25.195 26.653 >> 840POS POS 1426 26.656 24.646 27.207 >> 841POS POS 1427 27.493 24.378 26.671 >> 842POS POS 1428 25.704 28.084 24.322 >> 843POS POS 1429 26.024 28.033 24.522 >> 844POS POS 1430 25.690 27.436 25.511 >> 845POS POS 1431 25.499 26.486 25.378 >> ............................................................... upto 1553 >> particles then, >> 968NEG NEG 1554 27.665 27.041 24.226 >> 969NEG NEG 1555 27.770 25.717 24.582 >> 970NEG NEG 1556 27.165 25.469 26.884 >> 971NEG NEG 1557 26.602 25.231 27.215 >> 972NEG NEG 1558 27.309 24.502 27.300 >> 973NEG NEG 1559 27.075 25.317 25.083 >> 974NEG NEG 1560 26.927 25.837 25.127 >> 975NEG NEG 1561 26.247 26.641 24.480 >> 976NEG NEG 1562 25.888 26.676 24.614 >> 977NEG NEG 1563 25.773 27.276 25.174 >> 978NEG NEG 1564 25.345 26.065 25.614 >> 979NEG NEG 1565 24.862 26.307 25.737 >> 980NEG NEG 1566 27.642 26.470 26.780 >> 981NEG NEG 1567 26.721 27.065 26.145 >> 982NEG NEG 1568 26.398 26.984 25.969 >> 983NEG NEG 1569 26.291 25.493 26.397 >> 984NEG NEG 1570 26.029 24.681 26.249 >> 985NEG NEG 1571 26.374 23.945 26.814 >> 986NEG NEG 1572 26.551 24.207 25.873 >> 987NEG NEG 1573 27.184 23.760 24.934 >> 988NEG NEG 1574 25.102 22.440 25.649 >> 989NEG NEG 1575 23.763 24.119 26.999 >> ..........................1624 particles ... >> >> >> >> topology >> ........................................... >> ................................... >> [ moleculetype ] >> Neutral 1 >> >> [ atoms ] >> 1 NEU 1 NEU NEU 1 >> >> [ moleculetype ] >> Positive 1 >> >> [ atoms ] >> 1 POS 1 POS POS 1 >> >> [ moleculetype ] >> Negative 1 >> >> [ atoms ] >> 1 NEG 1 NEG NEG 1 >> >> [ moleculetype ] >> SS1 1 >> >> [ atoms ] >> 1 C 1 B1 C 1 >> 2 SA 1 S1 SA 2 >> 3 P 1 P1 P 3 >> 4 T 2 B2 T 4 >> 5 SA 2 S2 SA 5 >> 6 P 2 P2 P 6 >> 7 G 3 B3 G 7 >> 8 SA 3 S3 SA 8 >> 9 P 3 P3 P 9 >> 10 G 4 B4 G 10 >> 11 SA 4 S4 SA 11 >> 12 P 4 P4 P 12 >> 13 A 5 B5 A 13 >> 14 SA 5 S5 SA 14 >> >> The starting coordinates in gro file belong to molecule SS1 in topology >> file. As you can see, the coordinates for NEU, POS and NEG particles are >> towards the end in gro file but I am defining these particles in the >> beginning of topology file. Please let me know if this is ok or is it wrong >> ? And how can I check. >> >> > The only order that is pertinent is that of the [molecules] directive in > the .top file. It must match that of the coordinate file. If not, grompp > will exit with a fatal error. That's a fairly obvious way to check :) > > -Justin > > Thanks, >> Nimesh >> >> > -- > ======================================== > > 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 list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > 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/Support/Mailing_Lists > -- Nimesh Jain Graduate Student Biomedical Engineering Northwestern University
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! 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/Support/Mailing_Lists
