AMBER Archive (2004)

Subject: Re: AMBER: ptraj and dipoles

From: David A. Case (case_at_scripps.edu)
Date: Fri Feb 06 2004 - 01:11:50 CST

On Thu, Feb 05, 2004, Herbert Georg wrote:

> I would like to check the unit of the dipole moment given by the
> 'vector' command of ptraj??
> The manual says it is not normalized. What does it mean? If the dipole
> is calculated with the formula:
>
> dipole = sum_over_the_atoms_in_the_mask ( charge[i]*position_vector[i] )
>
> and the mask is neutral, then I don't understand why the dipole vector
> must be normalized.

The manual doesn't say it must be normalized; it says it is not normalized.
But that might be confusing, and you should ignore the comment in the manual
about normalization. The main point is that the dipoles are not converted to
common units (e.g. Debye).

..dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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