AMBER Archive (2004)

Subject: Re: AMBER: Dipole moment changes during MD

From: Jiten (jiten_at_postech.ac.kr)
Date: Fri Apr 09 2004 - 13:05:01 CDT

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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