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

Berk Hess hess at cbr.su.se
Fri Mar 11 19:19:08 CET 2011

On 03/11/2011 07:10 PM, David van der Spoel wrote:
> On 2011-03-11 17.39, Berk Hess wrote:
>> Hi,
>> Sound interesting, but I don't understand what x, y and z would mean.
>> Are those linked to the reference molecule coordinate frame?
>> g_densmap does that in 2D, in which case you can still visualize things
>> easily. But I can see 3D can be necessary in some cases.
> And how does this compare to g_sdf and g_spatial? It would be great if 
> these tools were merged into some kind of small library, avoiding the 
> overlap in the code and more modular.

On the other hand we don't want bloated tools with too many options, 
several of which
are unreliable and the user doesn't know any more which output he/she 
can trust.

There have been many issues with some of these tools (g_densmap works 
correctly though).
But not duplicating functionality is very important though.


> Something like this is implemented in g_dipoles as well.
>> Berk
>> On 03/11/2011 05:22 PM, Shirts, Michael (mrs5pt) wrote:
>>> 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

More information about the gromacs.org_gmx-developers mailing list