[gmx-developers] g_dipole molecule index

[Florian Dommert]

On 06.03.2009, at 09:31, Roland Schulz <roland at utk.edu> wrote:

> On Fri, Mar 6, 2009 at 3:00 AM,  <hessb at mpip-mainz.mpg.de> wrote:
>>> Roland Schulz wrote:
>>>> Hi,
>>>>
>>>> is there a reason why g_dipole uses a molecule index file and not  
>>>> an
>>>> atom index file? I think the later would be more general and would
>>>> also allow e.g. to to the analysis based on residues not molecules.
>>>>
>>>> Roland
>>>>
>>> Yes, because one is usually interested in the molecular dipole,  
>>> and e.g.
>>> for polarizable molecules can make a dipole distribution. However,  
>>> since
>>> the notion of molecules has disappeared from the topology the code
>>> probably needs to be updated.
>>>
>>> --
>>> David van der Spoel, Ph.D., Professor of Biology
>>
>> Hi,
>>
>> The notion of molecules has not changed at all.
>>
>> Also, g_dipoles reads atom indices, not molecule indices.
>> Roland, why do you think it reads molecule indices?
>>
>> I have changed this a while ago and I always use g_dipoles
>> without and index file and selected SOL only.
>
> Yes I didn't write it well. The index contains atom numbers but these
> are then translated into molecule index. Thus one can not select parts
> of a molecule. I would like to do the correlation of residue dipoles.
> Since g_current only does autocorrelation I think Flo's tip doesn't
> help.
>
Hi,
g_current is very flexible and can calculate the molecular and  
translational dipole moment of a molecule and i think also on a set of  
atoms. So you can determine the correlation afterwards by yourself.
Cheers
Flo
> Roland
>
>
>
> -- 
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> 865-241-1537, ORNL PO BOX 2008 MS6309
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