I did MD and now I want to separate the “frames” in pdb format of each 1ns for my 11ns simulation. I downloaded the VMD, but I cant save coordinates.
I’m not sure about VMD but if you want to extract frames from your trajectory file and put them into pdb files you can just use gmx trjconv. the command looks like this:
gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o 1ns.pdb -dump 1000.
-s: .tpr file
-f: trajectory file .xtc or .trr
-o: what you want to name the file and the format to store it in.
-dump: the frame you want to extract
For example 1ns is 1000 frames so the pdb file will contain the protein 1ns into the simulation.
This problem is not GROMACS relasted, but anyhow …
You need to select the row containing the molecular system you want to save. So, first click the line with 206708 atoms/12 frames (I can’t see the name of it) and then the menu item will be enabled.