Martini and energy calculation

User discussions
1

GROMACS version: 2019.6
GROMACS modification: No

Hey everyone,

I am facing an issue with my data analysis. I performed some molecular dynamics simulations with a few copies of ligands.

The simulations worked fine except for perhaps some bond rotation errors. Although sometimes the simulations stopped because of that, there were usually no issues for 100s of nanoseconds once they were restarted.

However, I did some analysis using the gmx energy tool, but I noted that only the first ligand displayed any sort of interaction with the rest of the system.

I checked the relevant coordinate (.gro) files, and nothing seemed to be out of order. Moreover, no other errors were observed other than the one mentioned before. Furthermore, I am not sure if gmx energy can calculate the interactions for the Martini model correctly.

Please share some feedback regarding this if feasible. Thank you very much.

2

What do you mean with bond rotation errors? Do you mean LINCS warnings?

gmx energy does not compute energies. It extracts energies computed by mdrun which are stored in the energy file.