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.<br><br>[ molecules ]<br> SS1 1<br> SS2 1<br> Neutral 536<br>
Positive 137<br> Negative 71<br><br>The particles in gro file are in this order. Thank you!<br><br><br><div class="gmail_quote">On Tue, Nov 9, 2010 at 12:37 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5"><br>
<br>
Nimesh Jain wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
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:<br>
<br>
gro file:<br>
1624<br>
1B1 C 1 22.237 30.408 26.522<br>
1B1 SA 2 22.348 30.033 26.829<br>
1B1 P 3 22.125 30.102 27.144<br>
2B2 T 4 21.852 30.069 26.468<br>
2B2 SA 5 21.824 30.189 26.949<br>
2B2 P 6 21.450 30.060 27.068<br>
3B3 G 7 21.778 29.762 26.361<br>
3B3 SA 8 21.321 30.008 26.724<br>
3B3 P 9 20.949 29.853 26.660<br>
4B4 G 10 21.629 29.470 26.321<br>
4B4 SA 11 21.026 29.716 26.325<br>
4B4 P 12 20.750 29.499 26.117<br>
5B5 A 13 21.487 29.154 26.338<br>
5B5 SA 14 20.990 29.299 25.943<br>
5B5 P 15 20.872 28.995 25.697<br>
6B6 G 16 21.351 28.838 26.366<br>
6B6 SA 17 21.165 28.798 25.747<br>
6B6 P 18 21.201 28.428 25.579<br>
7B7 A 19 21.229 28.513 26.410<br>
7B7 SA 20 21.416 28.303 25.825<br>
7B7 P 21 21.542 27.915 25.815<br>
8B8 T 22 21.195 28.076 26.416<br>
8B8 SA 23 21.574 27.883 26.158<br>
8B8 P 24 21.640 27.516 26.330<br>
9B9 A 25 20.912 27.888 26.523<br>
9B9 SA 26 21.488 27.595 26.632<br>
...................................................<br>
................................................... upto 880 particles then,<br>
295NEU NEU 881 27.530 28.268 24.349<br>
296NEU NEU 882 27.355 27.969 24.193<br>
297NEU NEU 883 27.623 27.876 23.941<br>
298NEU NEU 884 27.801 27.639 24.177<br>
299NEU NEU 885 27.473 27.507 24.322<br>
300NEU NEU 886 27.376 27.410 23.963<br>
301NEU NEU 887 27.316 26.930 24.121<br>
302NEU NEU 888 27.540 26.452 24.221<br>
303NEU NEU 889 27.266 26.353 23.979<br>
304NEU NEU 890 27.681 25.977 24.053<br>
305NEU NEU 891 27.538 25.708 24.281<br>
............................................................. upto 1416 particles then,<br>
831POS POS 1417 27.764 28.400 24.075<br>
832POS POS 1418 27.717 27.250 23.909<br>
833POS POS 1419 27.466 26.805 23.792<br>
834POS POS 1420 27.758 26.635 23.970<br>
835POS POS 1421 27.530 26.183 23.770<br>
836POS POS 1422 27.930 25.982 25.593<br>
837POS POS 1423 27.940 25.614 25.687<br>
838POS POS 1424 27.629 25.568 26.499<br>
839POS POS 1425 27.293 25.195 26.653<br>
840POS POS 1426 26.656 24.646 27.207<br>
841POS POS 1427 27.493 24.378 26.671<br>
842POS POS 1428 25.704 28.084 24.322<br>
843POS POS 1429 26.024 28.033 24.522<br>
844POS POS 1430 25.690 27.436 25.511<br>
845POS POS 1431 25.499 26.486 25.378<br>
............................................................... upto 1553 particles then,<br>
968NEG NEG 1554 27.665 27.041 24.226<br>
969NEG NEG 1555 27.770 25.717 24.582<br>
970NEG NEG 1556 27.165 25.469 26.884<br>
971NEG NEG 1557 26.602 25.231 27.215<br>
972NEG NEG 1558 27.309 24.502 27.300<br>
973NEG NEG 1559 27.075 25.317 25.083<br>
974NEG NEG 1560 26.927 25.837 25.127<br>
975NEG NEG 1561 26.247 26.641 24.480<br>
976NEG NEG 1562 25.888 26.676 24.614<br>
977NEG NEG 1563 25.773 27.276 25.174<br>
978NEG NEG 1564 25.345 26.065 25.614<br>
979NEG NEG 1565 24.862 26.307 25.737<br>
980NEG NEG 1566 27.642 26.470 26.780<br>
981NEG NEG 1567 26.721 27.065 26.145<br>
982NEG NEG 1568 26.398 26.984 25.969<br>
983NEG NEG 1569 26.291 25.493 26.397<br>
984NEG NEG 1570 26.029 24.681 26.249<br>
985NEG NEG 1571 26.374 23.945 26.814<br>
986NEG NEG 1572 26.551 24.207 25.873<br>
987NEG NEG 1573 27.184 23.760 24.934<br>
988NEG NEG 1574 25.102 22.440 25.649<br>
989NEG NEG 1575 23.763 24.119 26.999<br>
..........................1624 particles ...<br>
<br>
<br>
<br>
topology<br>
...........................................<br>
...................................<br>
[ moleculetype ]<br>
Neutral 1<br>
<br>
[ atoms ]<br>
1 NEU 1 NEU NEU 1<br>
<br>
[ moleculetype ]<br>
Positive 1<br>
<br>
[ atoms ]<br>
1 POS 1 POS POS 1<br>
<br>
[ moleculetype ]<br>
Negative 1<br>
<br>
[ atoms ]<br>
1 NEG 1 NEG NEG 1<br>
<br>
[ moleculetype ]<br>
SS1 1<br>
<br>
[ atoms ]<br>
1 C 1 B1 C 1<br>
2 SA 1 S1 SA 2<br>
3 P 1 P1 P 3<br>
4 T 2 B2 T 4<br>
5 SA 2 S2 SA 5<br>
6 P 2 P2 P 6<br>
7 G 3 B3 G 7<br>
8 SA 3 S3 SA 8<br>
9 P 3 P3 P 9<br>
10 G 4 B4 G 10<br>
11 SA 4 S4 SA 11<br>
12 P 4 P4 P 12<br>
13 A 5 B5 A 13<br>
14 SA 5 S5 SA 14<br>
<br>
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.<br>
<br>
</blockquote>
<br></div></div>
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 :)<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks,<br>
Nimesh<br>
<br>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br><font color="#888888">
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</font></blockquote></div><br><br clear="all"><br>-- <br>Nimesh Jain<br>Graduate Student<br>Biomedical Engineering<br>Northwestern University<br>