I have an MD trajectory file in TIP3P water. I want to use the trajectory to create a 3D visualization of the density map (or average polarization density whichever is easier) of the Oxygen and Hydrogen of the closest water molecules to the molecular surface. How do I go about it? I saw something in chimera tutorial but got confused. Something like the figure 2 in this article http://pubs.acs.org/doi/abs/10.1021/jp709958f is what I need.
Dear Abhishek,
In selection menu of Chimera program select the protein (or ligand).Choose Zone option (selection menu) and select all residues within 5 A distance of your previous selection.Finally save this selection as a new PDB file.
Best
Chimera is just a visualizer program. Figure 2 is produced by a visulizer program but for analysis purposes you need to perform RDF (radial distribution function) analysis using ptraj as mentioned in your template paper. Simple instruction about RDF in :
http://www.orbital.ufms.br/public/journals/2/330
Best
RDF is done on a single axis, the distance from the center of the solute atom. I have done rdf's before. I guess I am not clear in my original message. I have a trajectory from MD simulation. I now need to find the average distribution of all the oxygen atoms in water molecule in a 3D space and show upto 3\AA, i.e. the diameter of water molecule in a nice 3D figure. I have been googling and I found an option called grid in AMBER tools cpptraj. I will read more and will post the solution once I get it. Thanks for your help.
Abhishek,
Figure 2 in that paper is density plot. You can easily do this type of analysis in VMD. To get density map, use the VolMap plugin. In "Selection" specify "water and oxygen" (or "water and hydrogen"), volmap type - "density", weights - "mass", check the box to average results for the entire trajectory, and output results to a file. You may also increase a bit the default values in the "atom size" field to get slightly smoother-looking results and in the "resolution" field to speed up calculations (at least for the initial test run). The result will be a 3D map, that you can visualize nicely in VMD.
If you want to get g(r), use the GofRGUI plugin. Don't use GPU-accelerated version for now (or, at least, make sure to compare the results to the CPU version).
In VMD, you can access both of these plugins under Extensions->Analysis menu. (The latter is called "Radial Pair Distribution Function g(r)" there).
http://www.ks.uiuc.edu/Research/vmd/plugins/volmapgui/
http://www.ks.uiuc.edu/Research/vmd/plugins/gofrgui/
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