From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Mar 25 2011 - 09:14:47 CDT

2011/3/25 Donovan B.T. <B.T.Donovan_at_soton.ac.uk>:
> 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??

no. VMD is a visualization and analysis tool.

the partial charges are part of the force field or are otherwise
computed assigned (e.g. wannier centers).

.gro and .xtc files do not contain charge information.

axel.

> 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
>>
>>
>
>

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