VMD-L Mailing List

From: Donovan B.T. (B.T.Donovan_at_soton.ac.uk)
Date: Fri Mar 25 2011 - 08:18:38 CDT

Hmm, I seem not be pulling out any charge information at all.

>> set selatoms [atomselect top "name OW and (resid 129)"]
>> $selatoms get charge
0.0

This should be a oxygen atom on a water. There seem to be no partial charges at all. There are .gro and .xtc files [not my simulations] used to create the VMD render . Is VMD not computing the partial charges on the atoms??

Thanks
________________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Pawe³ Kêdzierski [pawel.kedzierski_at_pwr.wroc.pl]
Sent: Friday, March 25, 2011 7:55 AM
To: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: measure dipole

On 24.03.2011 19:07, Donovan B.T. 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
>
This may be too obvious, but have you checked this?:

$sel get charge

> 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.
>
> Thanks
>
>