VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue May 11 2010 - 16:23:51 CDT

On Tue, May 11, 2010 at 4:35 PM, Edward Lyman <edward.lyman_at_gmail.com> wrote:
> Turns out the -debye flag works alright...it might instead be an issue with
> the -masscenter flag...here are the results of three calls to measure dipole
> ($water is a single water molecule):
>
> measure dipole $water
> 0.0162629652768 0.0496227815747 -0.485804975033
>
> measure dipole $water -debye
> 0.0781143456697 0.23834836483 -2.33342051506
>
> measure dipole $water -debye -masscenter
> 0.0162629652768 0.0496227815747 -0.485804975033

thanks for the files.

if this is with vmd 1.8.6, then it makes sense.
-masscenter only exists since vmd 1.8.7 and
the argument parser would choke on unknown
flags and forget about all of them.

in 1.8.7 this works fine. there may still be a bug
with computing the center of mass. i'll have to look closer.

for a molecule without a total charge the dipole
is independent of the point of reference.

cheers,
    axel.

>
> Thx,
> E
>
>
>
> On Tue, May 11, 2010 at 2:29 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> On Tue, May 11, 2010 at 3:47 PM, Edward Lyman <edward.lyman_at_gmail.com>
>> wrote:
>> > Dear all,
>> >
>> > According to the vmd manual, you can switch the output of "measure
>> > dipole"
>> > to units of debye with the flag "-debye". However, I get exactly the
>> > same
>> > result regardless of whether I use the -debye or the -elementary flag.
>> >
>> > Any thoughts on what is happening here?
>>
>> perhaps a typo.
>> what is the _exact_ command line that you use?
>>
>> cheers,
>>    axel.
>>
>>
>> > Thx,
>> > Ed
>> >
>> >
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
>> http://sites.google.com/site/akohlmey/
>>
>> Institute for Computational Molecular Science
>> Temple University, Philadelphia PA, USA.
>
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.