[gmx-users] confusion on energy for a system of protein sovated in water

[Ming Tang]

Dear lists,

After pulling a protein in water and performing mdrun -rerun, I found that G96Bond, G96Angle, COM-Pull-En and Potential energy extracted from the original system using g_energy -f ener.edr , and from the -rerun system using g_energy -f rerun.edr have different values.  Firstly, are those values the energy of the system? Secondly, why are they different?

Thanks,
Ming