{
  "id": 96713,
  "title": "dipole_moments and structures coordinates are not always in the same axis?",
  "url": "/competitions/champs-scalar-coupling/discussion/96713",
  "author_name": "Alexander Tronin",
  "post_date": "2019-06-22T09:09:28.572000",
  "votes": 2,
  "comment_count": 8,
  "views": 0,
  "content": "<p>Hi!</p>\n\n<p>If we look at dsgdb9nsd_000001 - CH4:\nall dipole moment coordinates are zeros and\nand all average H coordinates match to C coordinates,\nwhich makes perfect sense to me.</p>\n\n<p>Again, if we look at dsgdb9nsd_000007 - C2H6:\nall dipole moment coordinates are zeros and\nand all average H coordinates match to all average C coordinates,\nwhich again makes perfect sense to me.</p>\n\n<p>But!</p>\n\n<p>If we look at dsgdb9nsd_000002 and dsgdb9nsd_000003 - NH3 and H2O correspondingly:\nX and Y coordinates of dipole moment in both molecules are zeros, but average X and Y coordinates of H in each molecule do not match to the coordinates of the remaining atom.</p>\n\n<p>Does this still make sense? How?</p>",
  "messages": [
    {
      "id": 558405,
      "postDate": "2019-06-22T09:09:28.573Z",
      "content": "<p>Hi!</p>\n\n<p>If we look at dsgdb9nsd_000001 - CH4:\nall dipole moment coordinates are zeros and\nand all average H coordinates match to C coordinates,\nwhich makes perfect sense to me.</p>\n\n<p>Again, if we look at dsgdb9nsd_000007 - C2H6:\nall dipole moment coordinates are zeros and\nand all average H coordinates match to all average C coordinates,\nwhich again makes perfect sense to me.</p>\n\n<p>But!</p>\n\n<p>If we look at dsgdb9nsd_000002 and dsgdb9nsd_000003 - NH3 and H2O correspondingly:\nX and Y coordinates of dipole moment in both molecules are zeros, but average X and Y coordinates of H in each molecule do not match to the coordinates of the remaining atom.</p>\n\n<p>Does this still make sense? How?</p>",
      "rawMarkdown": "Hi!\n\nIf we look at dsgdb9nsd_000001 - CH4:\nall dipole moment coordinates are zeros and\nand all average H coordinates match to C coordinates,\nwhich makes perfect sense to me.\n\nAgain, if we look at dsgdb9nsd_000007 - C2H6:\nall dipole moment coordinates are zeros and\nand all average H coordinates match to all average C coordinates,\nwhich again makes perfect sense to me.\n\nBut!\n\nIf we look at dsgdb9nsd_000002 and dsgdb9nsd_000003 - NH3 and H2O correspondingly:\nX and Y coordinates of dipole moment in both molecules are zeros, but average X and Y coordinates of H in each molecule do not match to the coordinates of the remaining atom.\n\nDoes this still make sense? How?\n",
      "votes": 2
    },
    {
      "id": 558627,
      "postDate": "2019-06-22T16:43:17.797Z",
      "content": "<p>Hi Alexander, I found out the same right now. Dipole moments looks very interesting to be involved into prediction process but axis in that file doesn't correspond to the axis in structure file. It can be converted for molecules that are symmetrical in at least 2 dimensions (in this case we can find for sure the direction of the dipole moment vector) but I have no idea what to do with other molecules. Do you find the way to handle it?</p>",
      "rawMarkdown": "Hi Alexander, I found out the same right now. Dipole moments looks very interesting to be involved into prediction process but axis in that file doesn't correspond to the axis in structure file. It can be converted for molecules that are symmetrical in at least 2 dimensions (in this case we can find for sure the direction of the dipole moment vector) but I have no idea what to do with other molecules. Do you find the way to handle it?"
    },
    {
      "id": 558413,
      "postDate": "2019-06-22T09:21:40.020Z",
      "content": "<p>Because methane and ethane and non-polar molecules, whereas ammonia and water are polar. \n<a href=\"https://en.wikipedia.org/wiki/Dipole\">https://en.wikipedia.org/wiki/Dipole</a></p>",
      "rawMarkdown": "Because methane and ethane and non-polar molecules, whereas ammonia and water are polar. \nhttps://en.wikipedia.org/wiki/Dipole",
      "replies": [
        {
          "id": 558439,
          "postDate": "2019-06-22T09:52:47.200Z",
          "content": "<p>Let me try to clarify my question :</p>\n\n<p>How come that X and Y coordinates of dipole moment of ammonia are zeros while averages of X and Y coordinates of hydrogens do not match to X and Y coordinate of N?</p>\n\n<p>How come that X and Y coordinates of dipole moment of water are zeros while averages of X and Y coordinates of hydrogens do not match to X and Y coordinate of O?</p>",
          "rawMarkdown": "Let me try to clarify my question :\n\nHow come that X and Y coordinates of dipole moment of ammonia are zeros while averages of X and Y coordinates of hydrogens do not match to X and Y coordinate of N?\n\nHow come that X and Y coordinates of dipole moment of water are zeros while averages of X and Y coordinates of hydrogens do not match to X and Y coordinate of O?"
        },
        {
          "id": 558458,
          "postDate": "2019-06-22T10:21:25.873Z",
          "content": "<p>Ah! I see the confusion... The XYZ coordinates of the structure give the position in real space of those atoms.\nThe dipole moment XYZ are not real space coordinates... they are the vector components of the dipole moment. So you can imagine drawing an arrow from the centre of the molecule (presumably at 0, 0, 0) to the XYZ given in the dipole file.</p>\n\n<p>Does that help?</p>",
          "rawMarkdown": "Ah! I see the confusion... The XYZ coordinates of the structure give the position in real space of those atoms.\nThe dipole moment XYZ are not real space coordinates... they are the vector components of the dipole moment. So you can imagine drawing an arrow from the centre of the molecule (presumably at 0, 0, 0) to the XYZ given in the dipole file.\n\nDoes that help?"
        },
        {
          "id": 558689,
          "postDate": "2019-06-22T18:35:15.910Z",
          "content": "<p>Are you saying that you are OK with the fact that for some molecules components of dipole moment vector provided in an axis that is different from coordinates of atoms are provided in?</p>\n\n<p>Don't you think that this makes dipole moment components to be to next to useless?</p>",
          "rawMarkdown": "Are you saying that you are OK with the fact that for some molecules components of dipole moment vector provided in an axis that is different from coordinates of atoms are provided in?\n\nDon't you think that this makes dipole moment components to be to next to useless?"
        },
        {
          "id": 558698,
          "postDate": "2019-06-22T18:47:33.060Z",
          "content": "<p>I'm not sure what you mean by axis, they are given in the same frame of reference.</p>\n\n<p>I guess individual dipole moments for each pair might be more informative than this \"global\" measure, but that's what we've got.</p>\n\n<p>I personally don't see how most of this extra information relates to the scalar coupling. I believe it can be calculated from the XYZ alone.</p>",
          "rawMarkdown": "I'm not sure what you mean by axis, they are given in the same frame of reference.\n\nI guess individual dipole moments for each pair might be more informative than this \"global\" measure, but that's what we've got.\n\nI personally don't see how most of this extra information relates to the scalar coupling. I believe it can be calculated from the XYZ alone.",
          "votes": 1
        },
        {
          "id": 558727,
          "postDate": "2019-06-22T20:12:22.217Z",
          "content": "<p>oops, yes, by axis I meant frame of reference</p>\n\n<p>also, I agree that this \"global\" measure my be not that useful, but what if the same is the case for a \"local\"  measure of magnetic shielding?</p>",
          "rawMarkdown": "oops, yes, by axis I meant frame of reference\n\nalso, I agree that this \"global\" measure my be not that useful, but what if the same is the case for a \"local\"  measure of magnetic shielding?"
        }
      ]
    },
    {
      "id": 558436,
      "postDate": "2019-06-22T09:52:30.193Z",
      "rawMarkdown": "",
      "isDeleted": true
    }
  ],
  "comments": [
    {
      "id": 558627,
      "author_name": "Boris Silantev",
      "author_url": "",
      "post_date": "2019-06-22T16:43:17.797000",
      "content": "<p>Hi Alexander, I found out the same right now. Dipole moments looks very interesting to be involved into prediction process but axis in that file doesn't correspond to the axis in structure file. It can be converted for molecules that are symmetrical in at least 2 dimensions (in this case we can find for sure the direction of the dipole moment vector) but I have no idea what to do with other molecules. Do you find the way to handle it?</p>",
      "votes": 0,
      "replies": []
    },
    {
      "id": 558413,
      "author_name": "phucco",
      "author_url": "",
      "post_date": "2019-06-22T09:21:40.020000",
      "content": "<p>Because methane and ethane and non-polar molecules, whereas ammonia and water are polar. \n<a href=\"https://en.wikipedia.org/wiki/Dipole\">https://en.wikipedia.org/wiki/Dipole</a></p>",
      "votes": 0,
      "replies": [
        {
          "id": 558439,
          "author_name": "Alexander Tronin",
          "author_url": "",
          "post_date": "2019-06-22T09:52:47.200000",
          "content": "<p>Let me try to clarify my question :</p>\n\n<p>How come that X and Y coordinates of dipole moment of ammonia are zeros while averages of X and Y coordinates of hydrogens do not match to X and Y coordinate of N?</p>\n\n<p>How come that X and Y coordinates of dipole moment of water are zeros while averages of X and Y coordinates of hydrogens do not match to X and Y coordinate of O?</p>",
          "votes": 0,
          "replies": []
        },
        {
          "id": 558458,
          "author_name": "phucco",
          "author_url": "",
          "post_date": "2019-06-22T10:21:25.873000",
          "content": "<p>Ah! I see the confusion... The XYZ coordinates of the structure give the position in real space of those atoms.\nThe dipole moment XYZ are not real space coordinates... they are the vector components of the dipole moment. So you can imagine drawing an arrow from the centre of the molecule (presumably at 0, 0, 0) to the XYZ given in the dipole file.</p>\n\n<p>Does that help?</p>",
          "votes": 0,
          "replies": []
        },
        {
          "id": 558689,
          "author_name": "Alexander Tronin",
          "author_url": "",
          "post_date": "2019-06-22T18:35:15.910000",
          "content": "<p>Are you saying that you are OK with the fact that for some molecules components of dipole moment vector provided in an axis that is different from coordinates of atoms are provided in?</p>\n\n<p>Don't you think that this makes dipole moment components to be to next to useless?</p>",
          "votes": 0,
          "replies": []
        },
        {
          "id": 558698,
          "author_name": "phucco",
          "author_url": "",
          "post_date": "2019-06-22T18:47:33.060000",
          "content": "<p>I'm not sure what you mean by axis, they are given in the same frame of reference.</p>\n\n<p>I guess individual dipole moments for each pair might be more informative than this \"global\" measure, but that's what we've got.</p>\n\n<p>I personally don't see how most of this extra information relates to the scalar coupling. I believe it can be calculated from the XYZ alone.</p>",
          "votes": 1,
          "replies": []
        },
        {
          "id": 558727,
          "author_name": "Alexander Tronin",
          "author_url": "",
          "post_date": "2019-06-22T20:12:22.217000",
          "content": "<p>oops, yes, by axis I meant frame of reference</p>\n\n<p>also, I agree that this \"global\" measure my be not that useful, but what if the same is the case for a \"local\"  measure of magnetic shielding?</p>",
          "votes": 0,
          "replies": []
        }
      ]
    },
    {
      "id": 558436,
      "author_name": "",
      "author_url": "",
      "post_date": "2019-06-22T09:52:30.193000",
      "content": "",
      "votes": 0,
      "replies": []
    }
  ],
  "raw_markdown_by_id": {
    "558405": "Hi!\n\nIf we look at dsgdb9nsd_000001 - CH4:\nall dipole moment coordinates are zeros and\nand all average H coordinates match to C coordinates,\nwhich makes perfect sense to me.\n\nAgain, if we look at dsgdb9nsd_000007 - C2H6:\nall dipole moment coordinates are zeros and\nand all average H coordinates match to all average C coordinates,\nwhich again makes perfect sense to me.\n\nBut!\n\nIf we look at dsgdb9nsd_000002 and dsgdb9nsd_000003 - NH3 and H2O correspondingly:\nX and Y coordinates of dipole moment in both molecules are zeros, but average X and Y coordinates of H in each molecule do not match to the coordinates of the remaining atom.\n\nDoes this still make sense? How?\n",
    "558627": "Hi Alexander, I found out the same right now. Dipole moments looks very interesting to be involved into prediction process but axis in that file doesn't correspond to the axis in structure file. It can be converted for molecules that are symmetrical in at least 2 dimensions (in this case we can find for sure the direction of the dipole moment vector) but I have no idea what to do with other molecules. Do you find the way to handle it?",
    "558413": "Because methane and ethane and non-polar molecules, whereas ammonia and water are polar. \nhttps://en.wikipedia.org/wiki/Dipole",
    "558436": ""
  }
}