[gmx-users] density map in 3 Dimension

[Justin A. Lemkul]

jagannath mondal wrote:
> Dear gromacs-users,
>  I thought of sending this query again as I did not get any response in 
> my last email.
>   I was wondering whether there is any way to calculate the 3D density 
> map of a particular selection of protein-water system ( say the water 
> near the protein backbone) in gromacs.
> I guess g_densmap provides a 2D map of the density. But I was looking 
> for 3D map of density. I presume it might have to do with calculating 
> volume of a space. But, I am not sure how to do it in gromacs.
> Any help will be appreciated.
> 

Two approaches come to mind:

1. Run g_densmap in all directions (invoking the -aver flag to change the 
dimension over which averaging is done), then somehow post-processing the output 
from the .xpm files into something meaningful.  That will involve a lot of 
scripting to parse out values from the .xpm files (which are translated from the 
various letters of the color scheme) and then assembling some sort of meaningful 
format for the output.  Doesn't sound to me like a trivial task, but perhaps it 
could be done.

2. Use g_select to define dynamic indices for water molecules that fit some 
geometric criterion, then feed these index groups into the individual frames of 
your trajectory (analyzed separately, since the index groups need not be of the 
same size), and again assemble some type of meaningful output from the 
probabilities or densities in (x,y,z) space.

I've never tried either of these nor do I have anything more specific to 
recommend, just the general workflow of thinking out loud ;)

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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