GROMACS version: 2021.5
GROMACS modification: Yes/No
I am new to molecular dynamics and using GROMACS.
I am simulating anime-based organic solvents using an OPLS-AA force field. I have generated all the parameters for the itp and gro files using LigParGen.
Energy minimization gives a value in the range of -1e5 for most compounds. However, for a few compounds, it is in -5e3; for some, it is positive in the e4 or e5 range.
I saw a similar thread with a person getting the same error: Energy minimization_ potential positive - User discussions - GROMACS forums (bioexcel.eu). But I get an error in the later stages of the simulation.
To check if I was getting molecular overlap, I reduced the number of molecules in these cases from a few hundred to 2. Even in this case, I was getting a positive potential energy. If I continue the simulation with this minimization, I get errors during the production stage of either the molecule drifting far away or bind angle becoming more than 30 degrees.
I am not sure how to proceed. At this point, I have already run the simulation for 40 compounds, and I would not want to change the forcefield for the remaining 20 compounds since I want some homogeneity in the forcefield.
Thank you