AMBER Archive (2004)

Subject: Re: AMBER: Dipole moment changes during MD

From: Jiten (jiten_at_postech.ac.kr)
Date: Fri Apr 09 2004 - 19:48:03 CDT

Dear Dr. Ross Walker,

Thanks a lot for your suggestons.

I am interseted to observe change in dipole moment of the water a bulk when disolving some ions in the solvent. For that what I need is first to calculate the dipole of the bulk solvent system (for example WATBOX216). When I dissolve some ions in the solvent, I wish to see the change in dipole of the bulk solvent, as the solvents in the first shell would allign towards the ion.

Is there a way to calculate the dipole of the bulk solvent (from the box) in amber7/8 ?

Thanks in advance,

JIten
  ----- Original Message -----
  From: Ross Walker
  To: amber_at_scripps.edu
  Sent: Saturday, April 10, 2004 6:56 AM
  Subject: RE: AMBER: Dipole moment changes during MD

  Dear Jiten,

  The way I implemented the measurement of dipoles in Amber 8 was to calculate them on the fly by calling a routine every time the results MD results were written to the mdout file. The code would look at the group specification for &dipoles in the input file and use this to determine how many different sets of dipoles to calculate and what atoms to include in each. For each dipole group chosen the code then looks up the X Y Z coordinates and charges (and also induced dipoles if running a polarisable calculation) for each atom in the group.

  Once you have this data calculating the dipole moment of the group is fairly simple. However, since the dipole moment is only non-ambiguous when the group is neutral the centre of mass of the group is first calculated. The dipole moment of the group is then calculated with respect to the group's centre of mass in order to remove this ambiguity. Note, if your groups are all neutral then you can skip this step.

  So, centre of mass for each variable is:
                  N
  X = (1/M)Sum{M(i)*X(i)}, Y = ..., Z = ....
                 i=1

  Next step is to subtract the centre of mass from the coordinates of each atom in your group. Then calculate the permanent dipole moment:
            N
  Px = Sum{q(i)*x(i)}, Py = ..., Pz = ....
           i=1

  This gives you the vector for your dipole moment. The magnitude of which ptot = sqrt(Px^2+Py^2+Pz^2).

  So, since your charges don't change in your simulation you should be able to post process your mdcrd file to obtain the permanent dipole moment. Note: Be careful with the units to ensure you get the answer in Debye.

  Note: 1 Debye = 0.2082267 electron angstroms
  Therefore 1 eA = 4.80246D

  With regards to calculating the dipole moment of your water I'm not sure what you hope to see by this. You should see the correct dipole magnitude and relative direction for each individual water molecule but the overall dipole moment for your solvent will not be the same as the dipole moment for a single water molecule since the waters will fluctuate over time. Hence at each point in time the individual dipoles will all be aligned in different directions and thus will cancel out. Unless of course something interesting is going on that is introducing order into your solvent and causing the dipoles to align.

  I hope this helps
  All the best
  Ross

  /\
  \/
  |\oss Walker

  | Department of Molecular Biology TPC15 |
  | The Scripps Research Institute |
  | Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
  | http://www.rosswalker.co.uk/ | PGP Key available on request |

      

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    From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of Jiten
    Sent: 09 April 2004 11:05
    To: amber_at_scripps.edu
    Subject: Re: AMBER: Dipole moment changes during MD

    Dear Dr. Ross Walker,

    Apart from checking the density of the solvent during the MD, I also wish to check the dipole as it also represents a property of the liquid. For example WATBOX216 (given along with the amber7 for TIP3 water model) must give a dipole moment of ~3 D. I am wondering how could I calculate the actual dipole moment of a solvent system.

    At the moment I use amber7 (planning to purchace amber8 soon).

    Your suggestions would be highly appreciated.

    With regards,

    JIten
      ----- Original Message -----
      From: Ross Walker
      To: amber_at_scripps.edu
      Sent: Saturday, April 10, 2004 1:48 AM
      Subject: RE: AMBER: Dipole moment changes during MD

      Dear Jiten,

      Which version of amber are you running? Amber v8 (Sander) includes the facility for printing permanent and induced dipole moments for any groups specified in the &dipoles namelist. This will print the dipole information to the mdout file every NTPR steps. See section 5.6.17 of the amber manual. Let me know if you have any problems getting it to work properly. I have tested it with a range of molecules but never actually tried calculating the dipole of the solvent. Note, if you are running a non-polarisable force field then you will simply get the permanent dipole. If you are running a polarisable force field then you will get permanent, induced and total dipoles.

      If you are using an older version of sander then you will have to do this manually yourself. It is possible that you could use ptraj to post process your trajectory file to calculate the permanent dipoles (but not the inducible ones) although I have not tried this.

      All the best
      Ross

      /\
      \/
      |\oss Walker

      | Department of Molecular Biology TPC15 |
      | The Scripps Research Institute |
      | Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
      | http://www.rosswalker.co.uk/ | PGP Key available on request |

------------------------------------------------------------------------
        From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of Jiten
        Sent: 08 April 2004 18:31
        To: amber_at_scripps.edu
        Subject: AMBER: Dipole moment changes during MD

        Dear Amber community,

        Could anyone suggest me how I can calculate the dipole moment of the solvent box during the course of the MD run / snapshots of MD run.

        Thanking you in advance,

        N. Jiten Singh
        C/O Prof. Kwang S. Kim
        Department of Chemistry
        Pohang University of Science and Technology
        San 31, Hyojadong, Namgu
        Pohang 790-784, Korea
        Phone : 82-54-279-5853 ( Lab ) / 279-4138 ( Appt )
        Fax : 82-54-279-8137 (or +82-54-279-3399)
        Web : http://csm.postech.ac.kr/ and http://www.postech.ac.kr/e
        Home Page : http://www.geocities.com/njs_19

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