VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Mar 24 2011 - 13:53:10 CDT

On Thu, Mar 24, 2011 at 2:07 PM, Donovan B.T. <B.T.Donovan_at_soton.ac.uk> wrote:
> Getting measure dipole to work.
>
> I have a membrane system with water and I want to select a region and compute the dipole moment at that region. For a test case I tried just a single lipid, where this is selected as follows:
>
>>>set sel [atomselect top "resid 1"]
>>>$sel get name
>
> gives....
>
> C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16 O17......etc etc
>
> now using
>>>measure dipole $sel
> 0.0 0.0 0.0
>
> and does this no matter what the molecule is including water. I'm not getting any measured vector for the measured dipole. It's probably something simple. Am I doing this the best way? I'm using the whole molecule as a test initially.

did you read in or assign the proper (partial) charges to the atoms?
this happens automatically for charmm based trajectories
when you load the matching .psf file.

>
> Thanks
>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.