AMBER Archive (2004)

Subject: RE: AMBER: Dipole moment changes during MD

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Apr 09 2004 - 11:48:29 CDT

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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