Increase in potential energy of peptide conformations Post MD run

User discussions
,
1

GROMACS version: 2023
GROMACS modification: No
I am very new to this field and do not have any idea how to resolve this. I am currently running MD simulation of different peptide sequences along with their conformations, however post run there is an increase in the potential energy of some conformations ,while some as stable, have tried changing the force field too but the issue remains unresolved. what could be the error and how do I troubleshoot it.

2

There is no rule that the potential energy of (part of) the system should go down during a simulation.

1 Like
3

But should’nt ideally the energy of the system be decreasing?

4

The potential energy not, the free energy yes.

5

okay thankyou :)