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Interpretation of PEO36.gro
- xudongh
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11 years 5 months ago - 11 years 5 months ago #1265
by xudongh
Interpretation of PEO36.gro was created by xudongh
Hello all,
I'm trying to figure out a bunch of the files right now and I'm particularly confused of what the following belong to a peo36.gro file is trying to tell me (file native to this website, under example and applications, polymers, peo36 in water)
1PEG O1 1 1.694 6.815 10.889 -0.0745 0.0749 -0.3560
1PEG O1 2 1.973 6.959 10.890 -0.0516 -0.0331 0.2117
1PEG O1 3 2.298 6.909 10.843 0.0670 0.2072 0.0554
1PEG O1 4 2.532 6.652 10.772 -0.1563 -0.2177 -0.0461
1PEG O1 5 2.540 6.337 10.912 0.4735 0.3265 0.4407
1PEG O1 6 2.481 6.028 11.031 -0.5627 -0.0623 0.3690
1PEG O1 7 2.413 6.023 11.330 0.0517 -0.1398 -0.0854
1PEG O1 8 2.342 6.295 11.486 -0.2653 -0.6131 0.5111
1PEG O1 9 2.593 6.499 11.585 -0.0674 0.5321 0.1004
1PEG O1 10 2.889 6.458 11.756 -0.0474 0.2097 0.0077
1PEG O1 11 2.891 6.153 11.859 0.3362 -0.1177 0.2739
1PEG O1 12 2.615 6.017 11.743 0.1592 -0.0417 -0.1226
1PEG O1 13 2.369 6.170 11.947 0.0794 0.2321 0.5678
1PEG O1 14 2.419 6.346 12.197 -0.0261 0.2319 0.1151
1PEG O1 15 2.280 6.282 12.475 0.1831 -0.4249 -0.0594
1PEG O1 16 2.122 6.048 12.630 -0.2610 0.2435 -0.0382
1PEG O1 17 1.971 5.765 12.605 0.1493 0.0992 -0.1620
1PEG O1 18 2.006 5.574 12.849 0.2675 -0.0078 -0.0297
1PEG O1 19 1.897 5.265 12.867 -0.0595 -0.2170 -0.2194
1PEG O1 20 1.943 5.126 13.128 -0.9640 0.2064 -0.4302
1PEG O1 21 2.064 5.196 13.428 -0.0658 0.1505 0.0140
1PEG O1 22 2.260 5.384 13.605 0.3498 0.3746 0.1943
1PEG O1 23 2.576 5.419 13.719 -0.6010 0.1651 -0.1080
1PEG O1 24 2.734 5.277 13.472 0.1480 -0.3541 -0.1360
1PEG O1 25 3.064 5.176 13.424 0.2656 0.2183 0.2267
1PEG O1 26 3.388 5.252 13.410 0.0822 -0.0902 -0.1385
1PEG O1 27 3.443 5.398 13.156 -0.0578 0.3067 0.1304
1PEG O1 28 3.358 5.348 12.848 -0.0588 0.2410 0.4184
1PEG O1 29 3.148 5.104 12.798 0.3820 -0.2375 0.0600
1PEG O1 30 2.956 4.986 13.039 0.1232 -0.0645 -0.3531
1PEG O1 31 2.747 4.822 13.218 0.0226 -0.1247 -0.3028
1PEG O1 32 2.456 4.918 13.352 0.1192 -0.0512 -0.1290
1PEG O1 33 2.359 4.959 13.666 -0.2163 -0.3354 -0.2143
1PEG O1 34 2.393 5.027 13.973 0.2063 -0.0343 0.0931
1PEG O1 35 2.680 5.156 14.096 0.1098 -0.0798 0.0510
1PEG O1 36 2.920 5.367 14.018 -0.0425 -0.0531 0.1077
1PEG O1 37 3.126 5.441 13.795 0.2088 -0.3830 0.0408
2PEG O1 38 1.794 11.767 3.371 -0.0043 0.2957 0.2960
2PEG O1 39 1.873 11.597 3.633 0.0735 0.2181 -0.1107
2PEG O1 40 1.689 11.318 3.670 -0.1017 0.1225 0.0205
2PEG O1 41 1.678 10.996 3.640 -0.1751 -0.2775 0.0738
2PEG O1 42 1.921 10.827 3.709 -0.1264 -0.3444 -0.1856
2PEG O1 43 2.012 10.685 3.984 0.3839 0.1670 -0.2607
2PEG O1 44 2.092 10.794 4.298 0.1373 0.1419 0.1764
2PEG O1 45 1.870 10.882 4.505 -0.0855 -0.0146 0.0017
2PEG O1 46 1.580 10.772 4.549 -0.0714 0.2506 0.7312
2PEG O1 47 1.393 10.748 4.274 -0.1183 0.1254 0.0070
2PEG O1 48 1.249 10.875 4.008 -0.2888 -0.1402 -0.0380
2PEG O1 49 0.937 10.942 4.056 -0.0288 0.0896 0.2035
2PEG O1 50 0.678 10.836 4.234 0.0351 -0.4117 -0.1549
2PEG O1 51 0.588 11.015 4.505 -0.1823 -0.0773 -0.0133
2PEG O1 52 0.760 11.283 4.563 0.1599 -0.0607 -0.1874
2PEG O1 53 0.731 11.510 4.341 -0.0928 -0.0671 0.2750
2PEG O1 54 0.506 11.696 4.221 -0.1664 -0.0221 -0.2074
2PEG O1 55 0.531 11.762 3.916 0.1553 -0.2272 0.4260
2PEG O1 56 0.383 11.637 3.657 -0.0930 -0.1411 0.0777
2PEG O1 57 0.330 11.351 3.543 0.0123 -0.0956 -0.2305
2PEG O1 58 0.123 11.106 3.501 -0.0351 -0.3663 0.0881
2PEG O1 59 -0.182 11.152 3.458 0.2863 0.4788 0.0447
2PEG O1 60 -0.225 11.429 3.369 -0.0253 -0.1416 -0.0413
2PEG O1 61 0.026 11.614 3.280 -0.1022 0.3271 -0.0410
2PEG O1 62 0.280 11.510 3.091 0.2518 0.1794 0.4055
2PEG O1 63 0.533 11.290 3.083 -0.0581 -0.1769 -0.0395
2PEG O1 64 0.602 11.151 2.785 -0.1446 -0.1595 -0.1070
2PEG O1 65 0.439 11.324 2.565 -0.0890 0.5106 0.1043
2PEG O1 66 0.166 11.500 2.546 -0.1816 -0.1742 -0.0621
2PEG O1 67 -0.123 11.435 2.396 -0.2300 -0.1779 -0.3175
2PEG O1 68 -0.175 11.136 2.356 -0.4230 0.4576 -0.0753
2PEG O1 69 -0.080 10.900 2.568 -0.3086 0.2769 -0.2818
2PEG O1 70 0.248 10.872 2.536 -0.6109 -0.1175 0.2972
2PEG O1 71 0.564 10.875 2.421 -0.0152 0.1206 -0.2490
2PEG O1 72 0.609 10.761 2.123 -0.2290 -0.3059 -0.5103
2PEG O1 73 0.308 10.693 2.036 -0.2733 -0.4276 -0.1540
2PEG O1 74 -0.001 10.837 2.000 -0.1644 0.0073 -0.1410
My question is: Is it saying that from bead 1 to 37, it contains all the same bead type named 1PEG? therefore, from 37 to 74 it contains all 2PEG type beads? and then the colums are x,y,z position of the beads? (In my case, is it okay to have all velocity =0)? and what does O1 in this case represent?
The actual file goes all the way up to 56PEG, what does that mean exactly? It contains 56 beads in total of the system or 56 types of beads? Because the .top file of this sytem shows PEG has molecule number of only 56.I'm confused.
Yet in the .itp file of this sytem, it shows only 37 bead definition and bonding order. ?
I'm trying to figure out a bunch of the files right now and I'm particularly confused of what the following belong to a peo36.gro file is trying to tell me (file native to this website, under example and applications, polymers, peo36 in water)
1PEG O1 1 1.694 6.815 10.889 -0.0745 0.0749 -0.3560
1PEG O1 2 1.973 6.959 10.890 -0.0516 -0.0331 0.2117
1PEG O1 3 2.298 6.909 10.843 0.0670 0.2072 0.0554
1PEG O1 4 2.532 6.652 10.772 -0.1563 -0.2177 -0.0461
1PEG O1 5 2.540 6.337 10.912 0.4735 0.3265 0.4407
1PEG O1 6 2.481 6.028 11.031 -0.5627 -0.0623 0.3690
1PEG O1 7 2.413 6.023 11.330 0.0517 -0.1398 -0.0854
1PEG O1 8 2.342 6.295 11.486 -0.2653 -0.6131 0.5111
1PEG O1 9 2.593 6.499 11.585 -0.0674 0.5321 0.1004
1PEG O1 10 2.889 6.458 11.756 -0.0474 0.2097 0.0077
1PEG O1 11 2.891 6.153 11.859 0.3362 -0.1177 0.2739
1PEG O1 12 2.615 6.017 11.743 0.1592 -0.0417 -0.1226
1PEG O1 13 2.369 6.170 11.947 0.0794 0.2321 0.5678
1PEG O1 14 2.419 6.346 12.197 -0.0261 0.2319 0.1151
1PEG O1 15 2.280 6.282 12.475 0.1831 -0.4249 -0.0594
1PEG O1 16 2.122 6.048 12.630 -0.2610 0.2435 -0.0382
1PEG O1 17 1.971 5.765 12.605 0.1493 0.0992 -0.1620
1PEG O1 18 2.006 5.574 12.849 0.2675 -0.0078 -0.0297
1PEG O1 19 1.897 5.265 12.867 -0.0595 -0.2170 -0.2194
1PEG O1 20 1.943 5.126 13.128 -0.9640 0.2064 -0.4302
1PEG O1 21 2.064 5.196 13.428 -0.0658 0.1505 0.0140
1PEG O1 22 2.260 5.384 13.605 0.3498 0.3746 0.1943
1PEG O1 23 2.576 5.419 13.719 -0.6010 0.1651 -0.1080
1PEG O1 24 2.734 5.277 13.472 0.1480 -0.3541 -0.1360
1PEG O1 25 3.064 5.176 13.424 0.2656 0.2183 0.2267
1PEG O1 26 3.388 5.252 13.410 0.0822 -0.0902 -0.1385
1PEG O1 27 3.443 5.398 13.156 -0.0578 0.3067 0.1304
1PEG O1 28 3.358 5.348 12.848 -0.0588 0.2410 0.4184
1PEG O1 29 3.148 5.104 12.798 0.3820 -0.2375 0.0600
1PEG O1 30 2.956 4.986 13.039 0.1232 -0.0645 -0.3531
1PEG O1 31 2.747 4.822 13.218 0.0226 -0.1247 -0.3028
1PEG O1 32 2.456 4.918 13.352 0.1192 -0.0512 -0.1290
1PEG O1 33 2.359 4.959 13.666 -0.2163 -0.3354 -0.2143
1PEG O1 34 2.393 5.027 13.973 0.2063 -0.0343 0.0931
1PEG O1 35 2.680 5.156 14.096 0.1098 -0.0798 0.0510
1PEG O1 36 2.920 5.367 14.018 -0.0425 -0.0531 0.1077
1PEG O1 37 3.126 5.441 13.795 0.2088 -0.3830 0.0408
2PEG O1 38 1.794 11.767 3.371 -0.0043 0.2957 0.2960
2PEG O1 39 1.873 11.597 3.633 0.0735 0.2181 -0.1107
2PEG O1 40 1.689 11.318 3.670 -0.1017 0.1225 0.0205
2PEG O1 41 1.678 10.996 3.640 -0.1751 -0.2775 0.0738
2PEG O1 42 1.921 10.827 3.709 -0.1264 -0.3444 -0.1856
2PEG O1 43 2.012 10.685 3.984 0.3839 0.1670 -0.2607
2PEG O1 44 2.092 10.794 4.298 0.1373 0.1419 0.1764
2PEG O1 45 1.870 10.882 4.505 -0.0855 -0.0146 0.0017
2PEG O1 46 1.580 10.772 4.549 -0.0714 0.2506 0.7312
2PEG O1 47 1.393 10.748 4.274 -0.1183 0.1254 0.0070
2PEG O1 48 1.249 10.875 4.008 -0.2888 -0.1402 -0.0380
2PEG O1 49 0.937 10.942 4.056 -0.0288 0.0896 0.2035
2PEG O1 50 0.678 10.836 4.234 0.0351 -0.4117 -0.1549
2PEG O1 51 0.588 11.015 4.505 -0.1823 -0.0773 -0.0133
2PEG O1 52 0.760 11.283 4.563 0.1599 -0.0607 -0.1874
2PEG O1 53 0.731 11.510 4.341 -0.0928 -0.0671 0.2750
2PEG O1 54 0.506 11.696 4.221 -0.1664 -0.0221 -0.2074
2PEG O1 55 0.531 11.762 3.916 0.1553 -0.2272 0.4260
2PEG O1 56 0.383 11.637 3.657 -0.0930 -0.1411 0.0777
2PEG O1 57 0.330 11.351 3.543 0.0123 -0.0956 -0.2305
2PEG O1 58 0.123 11.106 3.501 -0.0351 -0.3663 0.0881
2PEG O1 59 -0.182 11.152 3.458 0.2863 0.4788 0.0447
2PEG O1 60 -0.225 11.429 3.369 -0.0253 -0.1416 -0.0413
2PEG O1 61 0.026 11.614 3.280 -0.1022 0.3271 -0.0410
2PEG O1 62 0.280 11.510 3.091 0.2518 0.1794 0.4055
2PEG O1 63 0.533 11.290 3.083 -0.0581 -0.1769 -0.0395
2PEG O1 64 0.602 11.151 2.785 -0.1446 -0.1595 -0.1070
2PEG O1 65 0.439 11.324 2.565 -0.0890 0.5106 0.1043
2PEG O1 66 0.166 11.500 2.546 -0.1816 -0.1742 -0.0621
2PEG O1 67 -0.123 11.435 2.396 -0.2300 -0.1779 -0.3175
2PEG O1 68 -0.175 11.136 2.356 -0.4230 0.4576 -0.0753
2PEG O1 69 -0.080 10.900 2.568 -0.3086 0.2769 -0.2818
2PEG O1 70 0.248 10.872 2.536 -0.6109 -0.1175 0.2972
2PEG O1 71 0.564 10.875 2.421 -0.0152 0.1206 -0.2490
2PEG O1 72 0.609 10.761 2.123 -0.2290 -0.3059 -0.5103
2PEG O1 73 0.308 10.693 2.036 -0.2733 -0.4276 -0.1540
2PEG O1 74 -0.001 10.837 2.000 -0.1644 0.0073 -0.1410
My question is: Is it saying that from bead 1 to 37, it contains all the same bead type named 1PEG? therefore, from 37 to 74 it contains all 2PEG type beads? and then the colums are x,y,z position of the beads? (In my case, is it okay to have all velocity =0)? and what does O1 in this case represent?
The actual file goes all the way up to 56PEG, what does that mean exactly? It contains 56 beads in total of the system or 56 types of beads? Because the .top file of this sytem shows PEG has molecule number of only 56.I'm confused.
Yet in the .itp file of this sytem, it shows only 37 bead definition and bonding order. ?
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- djurre
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11 years 5 months ago #1270
by djurre
Replied by djurre on topic Interpretation of PEO36.gro
All this information (about how a .gro file is build-up) you can find in the Gromacs user manual.
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- xudongh
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11 years 5 months ago #1273
by xudongh
Replied by xudongh on topic Interpretation of PEO36.gro
@djurree,
I looked in the gromacs manual which describes atomistic representation of gro file
But I'm interested in coarse grain bead representation..
Thanks
I looked in the gromacs manual which describes atomistic representation of gro file
But I'm interested in coarse grain bead representation..
Thanks
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- djurre
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- Posts: 272
11 years 5 months ago #1275
by djurre
Replied by djurre on topic Interpretation of PEO36.gro
There is no difference, every field/column has the same function.
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