I ran a molecular dynamics simulation of an apo-ion channel for 15ns on NAMD. I'd like to look at the diameter of the ion channel at different intervals to examine the opening and closing of the channel.
The first thing that you can do is to use VMD; you have to select two object of the channel and monitoring the changing in distance between them during the simulation ( it is like to check the diameter in a determinate section of the channel).
I kind of did that. I tried to observe the bond length between two AA residues at the top and bottom of the channels. But is there a way I could measure the exact diameter?
Hi, I think you can use Tcl scripts to extract xyz coordinates of atoms that you want to consider in each frame, and then using xyz to calculate the distances. The distances can be calculated directly via Tcl scripts; however, the calculation may be failed if it calculates for a large number of atoms and/or frames. I find it is easier to calculate using a programing language such as Fortran, C++.
I hope this answer will help.
Goodluck.
Chanh Minh Thi Le can you please help me what will be tcl script for xyz coordinates? and also how can i utilize that tcl scripts?
You also can use an extension titled "HOLE". This can readily give the diameter of the channel
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