[gmx-developers] Any interest in a g(x, y.z) functionality for g_rdf?

[chris.neale at utoronto.ca]

Dear Michael:

g_sdf actually does the fitting within the program. I wrote g_spatial  
for the simple reason that I wanted to take full control of the  
fitting myself via trjconv (often in relatively complex trjconv/trjcat  
operations). I am not adverse to allowing g_spatial to do more of its  
own fitting, but I think that keeping the ability to create a sdf from  
a preprocessed trajectory is still very useful in some cases.

Quoting "Shirts, Michael (mrs5pt)" <mrs5pt at eservices.virginia.edu>:

> g_spatial looks like it has the correct capabilities - though a big of a
> pain - it really should be set up so that the alignment can be done more
> automatically.  Sorry for not looking more carefully!
>
> Best,
> ~~~~~~~~~~~~
> Michael Shirts
> Assistant Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434)-243-1821
>
>
>> From: "chris.neale at utoronto.ca" <chris.neale at utoronto.ca>
>> Reply-To: Discussion list for GROMACS development   
>> <gmx-developers at gromacs.org>
>> Date: Fri, 11 Mar 2011 12:59:46 -0500
>> To: "gmx-developers at gromacs.org" <gmx-developers at gromacs.org>
>> Subject: Re: [gmx-developers] Any interest in a g(x, y.z) functionality for
>> g_rdf?
>>
>> g_spatial does this for a single solute. A bizarre hacking of trjconv
>> and trjcat with .ndx file reordering could be used to do this with
>> g_spatial and a final .xtc file that is Nwat*Nframes. Not perfect, but
>> can be done right now without coding if I understand your interest
>> correctly.
>>
>> Chris.
>>
>> Quoting "Shirts, Michael (mrs5pt)" <mrs5pt at eservices.virginia.edu>:
>>
>>> Hi, all-
>>>
>>> Is there any interest in a g(x,y.z) functionality for g_rdf?  For many
>>> molecules, the liquid structure can be more complicated, and the ability to
>>> visualize it in three dimensions could be useful.  We're looking at this in
>>> my lab, and were thinking about just writing an easier postprocessing
>>> script, but if there is more demand for it, we can implement it in Gromacs
>>> as well.
>>>
>>> Best,
>>> ~~~~~~~~~~~~
>>> Michael Shirts
>>> Assistant Professor
>>> Department of Chemical Engineering
>>> University of Virginia
>>> michael.shirts at virginia.edu
>>> (434)-243-1821
>>>
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>>
>>
>>
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