I was able to calculate the number of contacts at a certain cut off using both NAMD and Gromacs. But I have no idea about calculating it on a certain direction (I want it on -Z direction) from a referenced atom.
Any help will be appreciated.
Thank you
Can you edit the code? If you can, replace the equation for calculating XYZ distance with the equation for calculating Z distance.
The XYZ distance is: (deltaX**2 + deltaY**2 + deltaZ**2)**0.5
The Z distance is: deltaZ
Dear Martin
I understand what you are trying to say. But I want to restrict in -Z direction only. If I take deltaZ then it calculate all the distance from all other atoms in Z direction. Correct me If I am wrong. Here is my tcl scripts for calculating contacts within a certain cut off.
mol load pdb system.pdb trr ../topol.trr
set outfile [open output.txt w]
set nf [molinfo top get numframes]
set P2 [atomselect top "resname SOL"]
set P1 [atomselect top "resid 283"]
for {set i 0} {$i
You will need to replace "set contact..." line with a new code, in which you calculate deltaZ = Z2 - Z1, where Z2 is P2's Z and Z1 is P1's Z, and if deltaZ < 0, then P2 lies in -Z (minus Z) direction with respect to P1.
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