[gmx-users] RE: gro file and topology files
Nimesh Jain
nimeshjain2010 at u.northwestern.edu
Tue Nov 9 20:02:34 CET 2010
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 <jalemkul at vt.edu> 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
>
> ========================================
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--
Nimesh Jain
Graduate Student
Biomedical Engineering
Northwestern University
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