[gmx-users] Potential energy reported by gmx energy command

[David van der Spoel]

Den 2018-06-28 kl. 09:03, skrev atb files:
> Hello experts, I did a LJ particles simulation, where I simulated two systems, 100 particle and 400 particle. For 100 particles energy is: Energy                      Average   Err.Est.       RMSD  Tot-Drift ------------------------------------------------------------------------------- Potential                  0.126288      0.029   0.615731 -0.0324041  (kJ/mol) Kinetic En.                 337.039       0.24    27.6568   0.443176  (kJ/mol) Total Energy                337.165       0.22    27.6615   0.410771  (kJ/mol) For 400 particle energy is: Energy                      Average   Err.Est.       RMSD  Tot-Drift ------------------------------------------------------------------------------- Potential                  0.502517      0.042    1.34584   0.220501  (kJ/mol) Kinetic En.                    1359       0.82    56.1468   -1.24836  (kJ/mol) Total Energy                 1359.5       0.78    56.1548   -1.02787  (kJ/mol) Since both systems have exact same operating conditions, only particle number has been changed, the per particle energy should be same, right? Here I see the energies has become 4 times in the second case. Then what is meaning of reporting energies in "KJ/mol" ? There is nothing like my system is not fully equilibrated, I have thoroughly checked, the both systems are well equilibrated. Please help in understanding these energies. Thank you
> 
gmx energy does not know what your system is composed of. However the 
-nmol 400 flag may help.

-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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