GROMACS version:2019
GROMACS modification: Yes/No
Here post your question
While I was simulating an oxidized membrane and glucose molecule, I came across an error which reflects some atoms overlap.
To the best of my knowledge it can be solved via the following ways: omit some water molecules, inflating, soft-core. I have been told the third one would be the choice solution
but I couldn’t fathom it in the search I carried out.
I’d be obliged if you could help me with the matter in question.
What is atom 3917? How did you generate the starting structure? A slight movement of that atom or the molecule it is associated with, or the other atom/molecule it is overlapping will most likely solve the issue.
Actually, I’ve found this issue will be solve by replacing FLEX-SPC with SPC. Unfortunately I couldn’t find its force field files. I’d be grateful if you could help me.
It would also most likely be solved by moving atom 3917, the molecule associated with it, or the atom/molecules it is overlapping with. That is the easiest solution, unless there are other things going on here that you aren’t sharing.
Thanks for answering.
Actually, this overlap occurs for a lot of molecules and it doesn’t solve just by moving or omitting one molecule. and the error happens for other atoms as well.
If you have extensive atomic clashes throughout your system, you should find a more reliable way of constructing it. You might be able to soft-core your way out of it by modulating all interactions within the system, but that will be extremely slow and could become unphysical.
Thank you for your answer
Actually, I’m still learning groamacs and seek to enjoy the precious knowledge and experience shared by experts . I wrote the process/ details of my work and based on your guidance I managed to reconstruct my system. However I’d appreciate if you helped me with softcore by introducing sources for further learning and the like.
Dallas linked the relevant mathematical formulation above. The original reference for soft-core potentials is https://www.sciencedirect.com/science/article/pii/0009261494003971 but many subsequent studies have investigated methodological details with and without soft core. A simple Google search for “soft-core potential” turns up a huge amount of information. The Alchemistry wiki also has lots of practical advice.
