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.
http://www.icm.uu.se
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