Energy minimization for Berendsen thermostat (temp/Berendsen)+ NVE

Hello everyone,

Can we perform energy minimization for a system that utilizes the Berendsen thermostat (temp/Berendsen)+ NVE?

Yes you can.

Energy minimisation is independent of the time integration and thermostat. They are carried out sequentially and not concurrently.

Thank you for the reply.
I am doing the energy minimization sequentially. In my system I have two domains that need to be fixed (no thermostat applied), to fix this two domains during the minimization as well, I am using set force and set velocities as follows,

velocity anchor set 0.0 0.0 0.0
fix rigin_anch anchor setforce 0.0 0.0 0.0

velocity surface set 0.0 0.0 0.0
fix rigin_anch_surf surface setforce 0.0 0.0 0.0

minimize 1.0e-12 1.0e-12 1000 1000
unfix rigin_anch
unfix rigin_anch_surf

The problem is that the energy minimization changes my results and the temperature fluctuates a lot during the simulations, It seems that the Berensden thermostat is not working properly by doing the energy minimization.

This is my thermostat:

Velocity rescaling thermostat

fix berendsenreplacesmd mob temp/berendsen 300.0 300.0 $(500.0*dt)

RUN with time integrator

fix 1 mob nve

The temperature is fine during the simulation but later after 20000 steps goes up to 600 K

As stated before, the Molecular Dynamics steps in you simulation (i.e. the update of the atoms positions by the NVE + the rescalling of the atoms velocities by the fix Berendsen) occur AFTER the minimization step. Therefore the Berendsen thermostat has nothing to do with the minimization.

What do you mean by that ? This is too vague, it could mean many different things.