From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Aug 13 2012 - 04:45:16 CDT

On Mon, Aug 13, 2012 at 11:38 AM, Francesco Pietra
<chiendarret_at_gmail.com> wrote:
> List added, sorry for previous mail

please make it a habit. it is very annoying
to have to remind people all the time.

>> Axel: I don't understand what you mean. I am not dealing with MD,
>> rather with ab initio, and DFT, calculations. Just drawn a system - as
>> above - collected the Cartesian coordinates, and subjected to the ab
>> initio, or DFT, code. Correctly when the charge is set to +1. I
>> thought that VMD, with the above script, reports the charge correctly.
>> I must be misusing VMD, or I am completely out the way.

so if you are not feeding VMD any information, where should it come from?
you don't say in what format you read in data before you run your script.

VMD is a *visualization* and *analysis* tool. it has absolutely no knowledge
of chemistry, only a little bit of protein oriented heuristics here and there.

in other words. the total charge will *always* be zero unless you set the
individual charges of the atoms some something, eg. through loading a
suitably generated file, which contains the respective charge information.

that is what i meant with GI-GO,
    axel.

>>
>> thanks
>> francesco
>>
>>
>>>
>>> GI-GO
>>>
>>> axel
>>>
>>>
>>>>
>>>> francesco pietra
>>>
>>>
>>>
>>> --
>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>>> International Centre for Theoretical Physics, Trieste. Italy.

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.