[gmx-developers] g_dipole molecule index

[Roland Schulz]

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.

Roland



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