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

atb files atbfiles at zoho.com
Wed Jul 4 11:20:19 CEST 2018

Thanks Prof. David, now my energies are making some sense and they are following the trend that, with increase in particle number RMSD decreases by (N)^1/2 for LJ fluid. If -nmol option is available, which may be used to calculate per particle averages, why default unit of "KJ/mol" has been used, which now looks very confusing. Please help Yogi ---- On Fri, 29 Jun 2018 01:31:47 +0530 David van der Spoel <spoel at xray.bmc.uu.se> wrote ---- 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

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