[gmx-users] gmx spatial

[Dallas Warren]

I would look at what you are using for the reference atoms around
which the SDF is generated. Ideally they should be relatively rigid in
position relative to each other, otherwise the SDF doesn't make as
much sense.
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 16:57, Valerio Ferrario <valerio.ferrario at gmail.com> wrote:
> 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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