[gmx-users] Disparity in total energy between consecutive steps

[Felix Y Yang]

Hi all,


So I've been trying a series of runs of heating-active-site-of-protein, then NVE, then heating again, and NVE again. And I've seemed to notice that the total energy of the system between the end of the heating process and the beginning of a NVE step right after it is significantly different, namely dropping a lot in total energy. The total energy seems to be retained a lot better between the end of an NVE step and the beginning of the next heating step.


Does anyone know what might be the cause of this? I have the protein position-restrained during the heating step, and released during the NVE step. The heating step is 3 ps, the NVE is 1 ns. For the heating step, I grouped the active site of the protein separately in an index file, and heated only that group, while the rest of the protein has the thermostat turned off. The other parameters in my mdp file are almost exactly the same for the heating and NVE processes.


Any feedback would be appreciated.


Thanks,


Felix Yang

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