[gmx-users] Simple L-J Particles' simulation

Mon Nov 3 19:36:01 CET 2003

Thanks, Dear  Paul !

This .gro file is obtained after EM (energy minimization) from a randomly produced .gro file. It did not work when mdrun.

I ran one more time on EM and get another .gro file as shown below, it did not work too when mdrun.

Do you know how what is it the problem?

Thanks for your advice.

------  

Argon

100

1Argon AR 1 1.028 0.808 1.010

2Argon AR 2 0.085 1.742 0.919

3Argon AR 3 1.423 0.954 0.283

4Argon AR 4 0.145 0.305 0.218

5Argon AR 5 1.954 0.259 1.575

6Argon AR 6 1.115 0.058 1.524

7Argon AR 7 1.396 1.736 1.537

8Argon AR 8 1.685 1.042 1.061

9Argon AR 9 1.647 1.386 0.240

10Argon AR 10 1.791 1.013 0.578

11Argon AR 11 1.015 1.830 0.234

12Argon AR 12 1.651 1.343 1.823

13Argon AR 13 0.320 1.743 1.789

14Argon AR 14 1.718 1.858 0.063

15Argon AR 15 1.016 0.349 0.849

16Argon AR 16 0.207 1.010 1.687

17Argon AR 17 0.886 1.356 2.029

18Argon AR 18 0.595 1.124 0.265

19Argon AR 19 1.336 1.109 0.742

20Argon AR 20 1.370 1.380 1.199

21Argon AR 21 1.089 0.667 0.510

22Argon AR 22 1.836 0.072 0.412

23Argon AR 23 0.447 0.991 1.222

24Argon AR 24 1.173 1.361 0.320

25Argon AR 25 1.938 1.685 0.491

26Argon AR 26 2.099 1.431 1.629

27Argon AR 27 1.407 0.079 0.206

28Argon AR 28 0.211 0.978 0.515

29Argon AR 29 0.988 0.901 0.119

30Argon AR 30 1.419 0.146 0.718

31Argon AR 31 0.389 0.178 1.496

32Argon AR 32 1.434 1.790 0.494

33Argon AR 33 1.275 0.956 1.842

34Argon AR 34 0.577 0.082 0.237

35Argon AR 35 1.133 1.328 1.599

36Argon AR 36 0.367 1.315 2.003

37Argon AR 37 0.214 0.519 0.628

38Argon AR 38 1.638 1.479 0.804

39Argon AR 39 1.699 0.844 2.025

40Argon AR 40 1.080 0.046 1.991

41Argon AR 41 0.472 1.263 0.816

42Argon AR 42 2.090 1.302 0.805

43Argon AR 43 0.361 0.456 1.092

44Argon AR 44 0.634 2.099 1.862

45Argon AR 45 0.007 0.811 0.930

46Argon AR 46 2.065 1.570 2.085

47Argon AR 47 0.321 1.483 1.241

48Argon AR 48 1.346 0.874 1.358

49Argon AR 49 0.291 0.813 0.059

50Argon AR 50 1.007 0.223 0.378

51Argon AR 51 0.838 0.451 2.087

52Argon AR 52 0.952 1.968 0.688

53Argon AR 53 1.971 0.675 0.299

54Argon AR 54 1.303 1.887 1.068

55Argon AR 55 0.610 0.615 0.362

56Argon AR 56 2.058 0.192 1.113

57Argon AR 57 0.605 1.828 1.427

58Argon AR 58 1.517 0.058 1.800

59Argon AR 59 0.812 0.443 1.264

60Argon AR 60 0.112 0.062 0.675

61Argon AR 61 1.451 0.656 0.837

62Argon AR 62 0.753 1.516 0.497

63Argon AR 63 0.503 0.641 1.552

64Argon AR 64 0.249 1.452 0.392

65Argon AR 65 0.873 2.090 1.139

66Argon AR 66 0.886 1.081 0.629

67Argon AR 67 1.813 1.592 1.253

68Argon AR 68 2.077 0.621 1.859

69Argon AR 69 0.695 1.666 0.982

70Argon AR 70 0.631 1.345 1.581

71Argon AR 71 1.780 0.959 1.565

72Argon AR 72 1.544 0.522 1.649

73Argon AR 73 1.043 0.526 1.670

74Argon AR 74 1.764 1.961 0.872

75Argon AR 75 0.459 1.854 0.602

76Argon AR 76 1.319 1.628 2.019

77Argon AR 77 0.057 0.665 1.389

78Argon AR 78 0.939 1.743 1.740

79Argon AR 79 1.316 0.358 1.216

80Argon AR 80 1.539 0.500 0.391

81Argon AR 81 0.592 0.235 0.697

82Argon AR 82 0.881 0.927 1.459

83Argon AR 83 0.082 1.909 1.389

84Argon AR 84 1.857 0.422 0.744

85Argon AR 85 0.154 1.928 0.230

86Argon AR 86 1.844 1.826 1.709

87Argon AR 87 0.591 0.761 0.820

88Argon AR 88 1.135 1.535 0.792

89Argon AR 89 0.892 1.265 1.127

90Argon AR 90 1.315 0.510 2.077

91Argon AR 91 1.647 0.007 1.320

92Argon AR 92 2.090 1.152 1.260

93Argon AR 93 1.743 0.564 1.204

94Argon AR 94 0.401 0.404 1.938

95Argon AR 95 0.406 2.070 1.055

96Argon AR 96 0.670 0.930 1.884

97Argon AR 97 0.081 0.035 1.912

98Argon AR 98 0.576 1.711 0.091

99Argon AR 99 1.796 0.317 2.087

100Argon AR 100 2.036 1.126 0.119

5.10000 5.10000 5.10000

Paul van Maaren <maaren at home.nl> wrote: 
On Mon, 3 Nov 2003, Albert Sun wrote:

> How does my .gro file (below) look strange? I am not in chemical area, greatly appreciate if you could advise me more detail.

If you look at it you will see that all particles are in one corner. Looks 
a bit strange to me.

-- 
Groeten,

Paul

---------------------------------
Do you Yahoo!?
The New Yahoo! Shopping - with improved product search
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20031103/5d760f47/attachment.html>