Hi,
I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the surface. How can I modify my gromacs trajectory file such that it has only the coordinates of atom in that region less than x nm (perpendicular to the surface). In other words, I want to collect all the frames of the trajectory with the updated coordinates of the atom only in that region for each frame?
Thanks,
Abhishek
Abhishek Soni
Hi Sir,
Thanks for the link. Even if I start with an index file, the atom number will change as the trajectory continues. I want to keep track of atoms only within a particular distance from my surface at each frame. How to do that?
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