[gmx-users] A simple question

Alex alexanderwien2k at gmail.com
Wed May 10 21:42:24 CEST 2017

Hello gromacs user,

Out of a well converged NVT simulation, I calculated the "Total-Energy =
Utot" as total internal energy of the system which contain three pieces (A,
B and water).
Then, using "gmx trjconv" and "gmx mdrun -rerun", "gmx energy", I
calculated the "Total-Energy" of each piece as U_A, U_B and U_W, using the
same method, I calculate again the U_AB, U_AB, U_AW ... , which is the
internal energy due to interaction between two pieces in the soup.

I expected that summing over U_A, U_B and U_W, U_AB ...., give me the
= Utot" of the system, but no combination of U_A, U_B and U_W, U_AB ...
could be equal to the "Total-Energy = Utot" !and the difference is really

Would you please let me know why so? or I am doing wrong somewhere?


Best regards,

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