[gmx-users] RE: gro file and topology files
Nimesh Jain
nimeshjain2010 at u.northwestern.edu
Tue Nov 9 19:33:50 CET 2010
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.
Thanks,
Nimesh
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101109/6295dfd5/attachment.html>
More information about the gromacs.org_gmx-users
mailing list