Re: [gmx-users] Potential energy reported by gmx energy command
If I am not wrong, you are suggesting the "per mol" in KJ/mol is total number of particles in the system. Which in special case for pure component system should give per particle energy scaled by Avogadro number, so for my case the RMSD decrease by (N)^1/2 should come out to be same whether I use or don't use -nmol option, or will the answer changes? On Wed, 04 Jul 2018 15:37:15 +0530 David van der Spoel wrote Den 2018-07-04 kl. 11:19, skrev atb files: > 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 Because we typically simulation mixtures, e.g. 100 methanol and 100 water or 1 protein in water. Then we can not decompose into molecules any more. On Fri, 29 Jun 2018 01:31:47 +0530 David van der Spoel 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-requ...@gromacs.org. > -- 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-requ...@gromacs.org. -- 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-requ...@gromacs.org.
Re: [gmx-users] Potential energy reported by gmx energy command
Den 2018-07-04 kl. 11:19, skrev atb files: 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 Because we typically simulation mixtures, e.g. 100 methanol and 100 water or 1 protein in water. Then we can not decompose into molecules any more. On Fri, 29 Jun 2018 01:31:47 +0530 David van der Spoel 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-requ...@gromacs.org. -- 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-requ...@gromacs.org.
Re: [gmx-users] Potential energy reported by gmx energy command
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 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-requ...@gromacs.org. -- 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-requ...@gromacs.org.
Re: [gmx-users] Potential energy reported by gmx energy command
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-requ...@gromacs.org.
