[gmx-users] gmx spatial

[Dallas Warren]

The values for the isosurface are a probability, just like for an RDF,
so negative values don't make any sense.

Visualise the trajectory you are analysing to see how the solute moves
around, and get a visual idea of if the SDF generated is consistent
with what you are seeing.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 28 June 2017 at 01:45, Valerio Ferrario <valerio.ferrario at gmail.com> wrote:
> Dear Users,
>
> I am trying to use the gmx spatial tool in order to understand how a solute
> interact with the protein. I performed the calculation following all the
> instructions (including the 2 trjconv steps). The trajectory obtained looks
> fine, and I calculated the sdf with the following command:
>
> gmx_mpi spatial -f CALBtrjvonv2.xtc -s CALBMpr-1.tpr -n X.ndx
>
> and selecting the protein and an atom of my solute molecules (in the index)
>
> but when I open the grid.cube file with vmd and I visualize it as
> isosurface I have the density function even within the protein core... I
> thought that the density should be just around the protein (in this case).
> Moreover I have just positive values for the isosurface, is that normal? Am
> I doing something wrong?
>
> Thanks a lot,
> Valerio Ferrario
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