GROMACS version: 2022.1
GROMACS modification: No
Here post your question:
Hello all I hope your well:).
for the above inquiry my generated system_inflated.gro file functions without errors when running the energy minimization, my questions is does the 6438 at the top of this file signify the total number of atoms in this file? I ask since the total number of atoms in this file is 6538, see below:
What you read here has nothing to do with anything. So you don’t have to read it. Thank you.
6438
1ACE CA 1 13.042 13.072 2.188
1ACE C 2 12.944 13.120 2.294
1ACE O 3 12.970 13.109 2.413
2GLY N 4 12.821 13.151 2.251
2GLY H 5 12.800 13.142 2.154
2GLY CA 6 12.718 13.197 2.342
2GLY C 7 12.681 13.089 2.441
2GLY O 8 12.681 13.111 2.562
3LYS N 9 12.675 12.964 2.391
3LYS H 10 12.694 12.949 2.294
3LYS CA 11 12.641 12.850 2.475
3LYS CB 12 12.623 12.725 2.390
3LYS CG 13 12.502 12.730 2.297
3LYS CD 14 12.490 12.602 2.215
3LYS CE 15 12.370 12.607 2.123
3LYS NZ 16 12.356 12.483 2.042
3LYS HZ1 17 12.276 12.491 1.983
3LYS HZ2 18 12.438 12.471 1.986
3LYS HZ3 19 12.345 12.404 2.103
3LYS C 20 12.749 12.829 2.579
3LYS O 21 12.720 12.819 2.698
4LYS N 22 12.875 12.846 2.539
4LYS H 23 12.892 12.872 2.444
4LYS CA 24 12.989 12.828 2.628
4LYS CB 25 13.120 12.836 2.550
4LYS CG 26 13.141 12.720 2.453
4LYS CD 27 13.273 12.734 2.380
4LYS CE 28 13.295 12.618 2.283
4LYS NZ 29 13.424 12.630 2.211
4LYS HZ1 30 13.435 12.553 2.149
4LYS HZ2 31 13.425 12.715 2.159
4LYS HZ3 32 13.499 12.630 2.277
4LYS C 33 12.985 12.934 2.738
4LYS O 34 12.992 12.901 2.856
5LEU N 35 12.949 13.057 2.700
5LEU H 36 12.927 13.074 2.604
5LEU CA 37 12.941 13.167 2.794
5LEU CB 38 12.916 13.298 2.721
5LEU CG 39 13.027 13.346 2.626
5LEU CD1 40 12.984 13.470 2.550
5LEU CD2 41 13.153 13.381 2.705
5LEU C 42 12.832 13.140 2.897
5LEU O 43 12.856 13.148 3.017
6ALA N 44 12.720 13.086 2.849
6ALA H 45 12.713 13.066 2.751
6ALA CA 46 12.607 13.056 2.936
6ALA CB 47 12.485 13.012 2.854
6ALA C 48 12.646 12.948 3.037
6ALA O 49 12.627 12.965 3.157
7LEU N 50 12.722 12.849 2.989
7LEU H 51 12.749 12.850 2.893
7LEU CA 52 12.766 12.740 3.074
7LEU CB 53 12.835 12.632 2.990
7LEU CG 54 12.747 12.558 2.888
7LEU CD1 55 12.831 12.464 2.802
7LEU CD2 56 12.641 12.475 2.959
7LEU C 57 12.859 12.792 3.182
7LEU O 58 12.839 12.764 3.300
8ALA N 59 12.947 12.885 3.144
8ALA H 60 12.947 12.915 3.049
8ALA CA 61 13.042 12.943 3.237
8ALA CB 62 13.142 13.033 3.162
8ALA C 63 12.968 13.021 3.345
8ALA O 64 12.992 13.000 3.464
9LEU N 65 12.864 13.093 3.304
9LEU H 66 12.840 13.092 3.207
9LEU CA 67 12.784 13.173 3.395
9LEU CB 68 12.683 13.258 3.320
9LEU CG 69 12.741 13.366 3.228
9LEU CD1 70 12.631 13.433 3.147
9LEU CD2 71 12.813 13.473 3.309
9LEU C 72 12.714 13.082 3.495
9LEU O 73 12.724 13.103 3.616
10ALA N 74 12.663 12.969 3.447
10ALA H 75 12.673 12.950 3.349
10ALA CA 76 12.594 12.873 3.530
10ALA CB 77 12.531 12.761 3.445
10ALA C 78 12.689 12.815 3.634
10ALA O 79 12.660 12.815 3.753
11LEU N 80 12.813 12.786 3.590
11LEU H 81 12.836 12.803 3.494
11LEU CA 82 12.914 12.730 3.678
11LEU CB 83 13.038 12.692 3.597
11LEU CG 84 13.021 12.579 3.495
11LEU CD1 85 13.148 12.561 3.413
11LEU CD2 86 12.990 12.448 3.564
11LEU C 87 12.949 12.830 3.787
11LEU O 88 12.946 12.796 3.906
12ALA N 89 12.958 12.958 3.750
12ALA H 90 12.942 12.982 3.654
12ALA CA 91 12.990 13.062 3.844
12ALA CB 92 13.011 13.196 3.772
12ALA C 93 12.881 13.075 3.949
12ALA O 94 12.908 13.073 4.068
13LEU N 95 12.755 13.064 3.904
13LEU H 96 12.740 13.048 3.806
13LEU CA 97 12.641 13.074 3.992
13LEU CB 98 12.511 13.075 3.912
13LEU CG 99 12.489 13.196 3.820
13LEU CD1 100 12.364 13.178 3.736
13LEU CD2 101 12.473 13.324 3.901
13LEU C 102 12.641 12.959 4.092
13LEU O 103 12.632 12.981 4.212
14LYS N 104 12.677 12.840 4.043
14LYS H 105 12.701 12.832 3.946
14LYS CA 106 12.682 12.722 4.127
14LYS CB 107 12.707 12.597 4.043
14LYS CG 108 12.593 12.561 3.948
14LYS CD 109 12.625 12.437 3.867
14LYS CE 110 12.511 12.401 3.772
14LYS NZ 111 12.541 12.279 3.692
14LYS HZ1 112 12.464 12.259 3.631
14LYS HZ2 113 12.623 12.294 3.637
14LYS HZ3 114 12.556 12.202 3.754
14LYS C 115 12.789 12.737 4.233
14LYS O 116 12.762 12.718 4.352
15LYS N 117 12.902 12.795 4.194
15LYS H 118 12.910 12.826 4.099
15LYS CA 119 13.014 12.815 4.285
15LYS CB 120 13.136 12.866 4.210
15LYS CG 121 13.197 12.763 4.114
15LYS CD 122 13.318 12.819 4.042
15LYS CE 123 13.378 12.718 3.947
15LYS NZ 124 13.497 12.772 3.876
15LYS HZ1 125 13.534 12.702 3.814
15LYS HZ2 126 13.471 12.853 3.823
15LYS HZ3 127 13.567 12.797 3.943
15LYS C 128 12.974 12.914 4.394
15LYS O 129 12.990 12.885 4.513
16ALA N 130 12.900 13.017 4.356
16ALA H 131 12.874 13.025 4.260
16ALA CA 132 12.855 13.119 4.449
16ALA CB 133 12.788 13.236 4.374
16ALA C 134 12.758 13.058 4.550
16ALA O 135 12.777 13.073 4.670
17NH2 N 136 12.672 12.970 4.501
17NH2 H1 137 12.674 12.948 4.404
17NH2 H2 138 12.606 12.926 4.561
+
128 lipids = 128 x 50 = 6400 lipid atoms + 138 residue atoms = 6538
Thanks:)