I'm still confused. Whether to determine the methylene blue orientation, I have to use the order parameter (gmx order) or the gmx angle?
I want to determine the orientation of the methylene blue adsorbed on the clay surface as in figure 7. I try compute gmx angle -f .xtc -n [] -ov[]. But the graph obtained does not match as shown in figure 7. Because of the command I input the angle to the time function.
Can you give me suggest?
Hi Ovi! I am afraid that in your simulation you get average values for the whole simulation which can mean that even the conformations when your molecule is not on the surface. In order to know orientations on the surface you shall add some constraint to that. I haven't seen a routine in gromacs doing that for you. I was analyzing orientations of cholesterol in different positions in lipid bilayers and that was done by my own code. Therefore, I suggest you to write the code which could show the distribution of orientations versus the Z-coordinate of the center of mass of your molecules. That would be some 3D plot (surface).
Inna Ermilova thank you madam. And the Z coordinate of the center of mass of the molecule that I should write down on the methylene blue or the clay surface?
You are wellcome, Ovi! Firstly, you shall determine which Z is the surface. Then you can calculate for all Z and plot it. Knowledge about the location of the surface will help you to make conclusions about orientations at the surface and far away from it.
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