Using VMD's inbuilt volmap plugin, I was able to generate a potential map (.dx) How do I generate electrostatic potential profile along the pore in the translocation axis (Voltage vs z distance as used in the 'Biophysical Journal, 88:3745–3761, 2005' paper.
The figures in the paper are added as an attachment.
Kindly look on this tutorial may be it helps
http://bionano.physics.illinois.edu/sites/default/files/ion-tutorial.pdf
You cannot do it directly in VMD. You will need to write a script (in any scripting language such as tcl, python, awk) to extract the V vs z data from the .dx file. Also, remember that the potential you get from .dx file is the reaction potential. So to get the total potential you need to add the applied potential to it
V_total= V_reaction+ z*V_applied/H,
where H is the height in z-direction.
@Aashish Bhat, Thanks for the answer, but I have difficulty in getting c) and d) mentioned in the figure. Profiles of electrostatic potentials along the pore. Voltage vs Distance plot. Thanks.
@Subin, Thank you so much for the information. How do I add the corresponding bias to the reaction potential (.dx) file? Is there any plug-in in MATLAB or in VMD, or should we write a script for that on our own? Thanks.
Here is a simple awk code that I wrote to convert "potential.dx" file into "potential.txt" file which has columns x, y, z, V. You can then use the "potential.txt" file to get the (V vs z) profile by averaging over appropriate x and y, and adding the applied potential.
awk 'BEGIN{ind=0}
(NR==2){Nx=$6; Ny=$7; Nz=$8}
(NR==3){ox=$2; oy=$3; oz=$4}
(NR==4){dx=$2}
(NR==5){dy=$3}
(NR==6){dz=$4}
(NR>8){for(c=1;c
Subin Sahu Thank for your code. Could you please explain the code that after (NR>8) part? Thank you again for your time.
From line number 9 to end of the file, the dx file list data in a 2D grid. Thus, an arbitrary data at (row=NR, column=c) is V(i,j,k) where i, j, and k are indices for x,y and z coordinates:
V(1,1,1) V(2,1,1) V(3,1,1)
V(4,1,1) V(5,1,1) V(6,1,1)
...
.... V(Nx,1,1) V(1, 2,1)
...
...
... V(Nx,Ny,1) V(1,1,2)
...
...
...
... V(Nx,Ny,Nz)
END
The i,j,k indices of a data point is determined by its position counter (ind) in the grid and the shape of the system (Nx,Ny,Nz). My code basically extracts the indices of each data point. Once you have indices it is trivial to get x,y,z coordinates.
Subin Sahu you mention that you mentioned that you average over the appropriate x, y and then add the potential. What does this mean? Essentially do you average the potential values based upon having the same z value? I am having difficulty understanding how to apply this.
Thank you so much for your help!
Hannah Burton The potential you get from VMD is the "induced potential" in the (x,y,z) grid, i.e you get V_induced(x,y,z).
When you average it over x & y you get V_induced(z).
You then have to add the applied potential V_applied(z) to get the total potential.
V_total(z) = V_induced(z)+V_applied(z)
Hello Subin Sahu thanks for responding so quickly!
Quick question, how does one get the applied potential to add to the system? Sorry I am quite new to this field!
Hannah Burton Generally constant electric field (E_applied say) is applied in MD simulations, so the applied potential will be V_applied(z) = E_applied * z + V_0. You can set the ground potential V_0 to zero or any constant. Also, you need to make the necessary unit conversion, e.g E_applied to volts/A if the unit of z is in A.
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