AMBER Archive (2004)

Subject: Re: AMBER: dipole moment in ptraj

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Sun Feb 08 2004 - 17:00:55 CST

> I would like to know the unit of the dipole moment given by ptraj
> through the 'vector' command, so that I could make the conversion the
> unit I use.

Although I did not add the "dipole" functionality to the vector command (I
don't think), it appears to be fairly simple. This can be seen by
perusing the source code in actions.c, transformVector(). In general, the
"vector" command produces vectors. The vector is, for the dipole, the

COM --> COM + sum(coordinates * charge)

COM is center of mass.

It is done separately for X, Y and Z coordinates. The coordinates are in
angstroms. The charge is the charge on each atom. The dipole moment is
not reported, however I think this is likely just the magnitude
of this vector, converted to the appropriate units.

I would suggest using or making a test case (of a small molecule or set of
particles) to compare what you would hand calculate to what you would get
through the procedure with ptraj. It is also possible to modify the ptraj
code to calculate this for you...

Good luck, and hopefully this will answer your question sufficiently such
that we will not have to be asked daily anymore :-)

\ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy, Depts of
| Medicinal Chemistry and of Pharmaceutics and Pharmaceutical Chemistry
| Adjunct Asst Prof of Bioengineering; Center for High Performance Computing
| University of Utah, 30 South 2000 East, Skaggs 201, Salt Lake City, UT 84112
|
| tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
\ BPRP295A / INSCC 418 http://www.chpc.utah.edu/~cheatham

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