VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue May 12 2009 - 08:47:43 CDT

On Tue, 2009-05-12 at 18:23 +0530, Suman Chakrabarty wrote:
> Hi,
>
> since I did not get any solution to the following problem, let me try

suman,

> to reframe my question. I have a hydrophobic molecule in water and
> would like to show the regions around the molecule where there is no
> water. How do I achieve this? Using volmap and volumeslice

what want to do is an ill defined problem. it is always difficult
to show the absence of something. also, i would doubt whether there
will be a significant void unless you are running an NVT ensemble
with negative pressure.

that all being said, the straightforward way to look into this would
be to compute (and show) the density distribution of your hydrophobic
molecule and the water around it with the molecule first being aligned
to a reference orientation and then computing the density map of the
water molecules. depending on the size and shape of your molecule,
simply computing radial distribution functions (g(r)) relative to
the water oxygen atoms could be sufficient, too.

> representation I can show this as slices, but I could not show all the
> regions together for the whole molecule. I have a feeling that the
> isosurface representation can probably do this, but I could not figure
> out how to show the regions with density range "0 to <some cut-off
> value)" around the solute.

actually, an isosurface shows the the volume enclosed from zero up to
the specified isovalue. have you considered that if you don't see what
you expect that the reason may be that you have not computed what you
think you are computing? this is more often than not the reason why
people are confused about how to use a representation. you always have
to keep in mind that VMD is programmed to be incredibly ignorant about
what a person's intents are and just does what it gets told to do. ;)

cheers,
   axel.

>
> Also, with the volmap type "distance", how is it possible to have a
> reference group (like solute) and calculate the distance map with the
> solvent molecules?
>
>
> Thanks and regards,
> Suman.
>
>
> On Sun, May 10, 2009 at 1:16 AM, Suman Chakrabarty
> <suman_at_sscu.iisc.ernet.in> wrote:
> > Hi,
> >
> > I intend to monitor the excluded volume of the solvent due to presence
> > of a solute along the trajectory. Using volmap I could generate the
> > density distribution graphically (VolumeSlice), but I need to know how
> > to use the grid data to compute the total excluded volume (no
> > solvent).
> >
> > Also, it seems VolumeSlice representation works only along three axes.
> > Is it possible to rotate the plane arbitrarily?
> >
> >
> > Regards,
> > Suman. 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.