[gmx-users] How to conserve total energy from a position-restrained step to a non-constrained step

[Felix Y Yang]

Hi all,

So I've noticed that the total energy of my system decreases every time I run an un-constrained production run immediately after a position-restrained heating step, most likely due to algorithms. I am attempting to string together multiple repeated steps of heating and running, and each period I am losing 1500kJ/mol by the whole system, forming a "staircase" pattern in my total energy vs time graph, which makes the whole concatenated process hard to evaluate. If I remove the position-restraints on my heating steps, the system starts rotating out of control. Is there a way to circumvent this loss of energy due to algorithms, or another way to complete one whole process that has heating turned on and off throughout the process?

Any feedback would be appreciated.

Thanks,
Felix Yang

Graduate Master's Student
Department of Chemistry & Biochemistry
University of California, San Diego