GROMACS version: 2022.1
GROMACS modification: No
I would like to simulate the effect of the binding of simple thiols on a gold surface. You can read a lot in publications and I wanted to try myself some simple MD simulations. The setup of Gromacs is done and I worked myself through some tutorials. Now I wanted to start by creating the initial system configuration file/topology file and faced my first problem.
My questions now:
- Is it possible to initialize the system in Gromacs directly or do I have to use another software?
- If I have to use another software, do you have any suggestions? BallView, PyChem, etc?
- I tried BallView and PyChem, but did not get any useful results (the atoms were not placed in one plane or I could not even find the needed atoms/molecules). Is there any tutorial which teaches you sort of what I need?
Any help is welcome!
Thanks in advance!