I want a good measure for water content around a wild type side chain, and then a measure around the glycated form of that side chain i.e., a comparison of two individual systems.
I think that Surface Distribution Functions as a description for the density of water as a function of the distance from the protein surface is a good idea. But I am puzzled by the "gmx rdf -surf" description in Gromacs. Is this an SDF calculations?
Gromacs yields y-values as high as 300, and I have no idea what that means. Is this an average or absolute, and what is the unit?
Also, consider the work in J Phys Chem B. 2008 September 25; 112(38): 12073–12080. doi:10.1021/jp802795a (see link) which yields an SDF in Figure 2a. Although the result looks similar to my test of Gromacs, the y-axis only goes up to 0.2 with units of "Number of water/Ang^3".
I have attached an image of "gmx rdf -surf mol" and "gmx rdf -surf res", what is it trying to describe? Thanks.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768875/pdf/nihms146616.pdf
Using "-surf" means the results will not be normalised i.e, "-norm" can't be used. That is why it is giving such high values.
Ok, thanks, Sayantan.
That leaves me with trying to find an actually Surface Distribution Function.
What would be the best way to quantify how much water is around a side chain?
Thanks
Anthony
Sounds like what you want is a coordination number, e.g. gmx rdf -cn or just integrate the RDF itself. The -surf option simply constructs a surface around the solute and uses that as the RDF reference rather than the individual atomic coordinates. Maybe what you're after is a spatial distribution function, e.g. gmx spatial? But that's sort of a qualitative assessment because the only output is a cube file with the spatial occupancies.
Hi Justin,
Thanks for your post. It was extremely useful. I just took a closer look at the rdf -h:
"Option -cn produces the cumulative number RDF, i.e. the average number of particles within a distance r." I'll give that a try. Plus, thanks for raising my awareness regarding gmx spatial, I'll look into that.
Thanks again.
hi Anthony,
if you can, try writing a code just using the trajectory. as it can be customised, you can find out the exact reason for such anomalous values.
thanks
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