[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
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