[gmx-users] Energy Conservation Conundrum

[Kruse, Luke E.(MU-Student)]

Hello Everyone,


I am a new user to gromacs and I am having trouble with energy conservation in my simulation. After I produced the (solvated and neutralized) configuration and respective topology files I performed an energy minimization that converged to single-precision machine accuracy.


After the minimization, I wanted to ensure that the system is conserving energy, so I performed a brief run with no thermo- or barostats in place, constraining only the H-bonds with the LINCS algorithm (lincs-order =4 and lincs-iter =4). I have tried decreasing the timestep from 2 fs to 1 fs and even 0.1 fs to no avail. Any recommendation?


Warm regards,

Luke