[gmx-users] gmx spatial

[Valerio Ferrario]

Yes, you are right, but the problem is that if I visualize the trajectory I
have the solute around the protein whereas with the spatial distribution
function I obtain density function around the protein as well as within the
protein core and this make no sense or at least is not convincing. Moreover
the trajectory seems very good, with the protein perfectly superposed and
with the same orientation in each trajectory step. Is there a way to define
the interaction? i.e. the 2 selected groups interacts when they are within
a given distance?

Best,
Valerio

2017-06-28 3:29 GMT+02:00 Dallas Warren <dallas.warren at monash.edu>:

> 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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