Re: [gmx-users] Re,problem with EM
On 11/20/12 1:04 PM, Ali Alizadeh wrote: Dear Justin Thank you for the quick reply Dear All users I want my energy minimization of my system is converged to considered value, when i do it, It is converged because it reachs to Fmax and i see this message : Steepest Descents converged to Fmax < 10 in 31702 steps Potential Energy = -1.6531438e+03 Maximum force = 9.8014317e+00 on atom 162 Norm of force = 2.9060462e+00 my result: http://alichemical.persiangig.com/document/em.jpg When i represent profile of potential energy by g_energy, i can't see my considered results, I should reach this result that this link is related to it, http://alichemical.persiangig.com/document/11.jpg That's right, I knew it but in your opinion, How can i get same result, What's the value of emtol for my system? Justin wrote: If you want to reproduce the results of an MD trajectory, you need to be doing MD, not EM. -Justin I do not know my emtol value, How can i determine it? emtol is simply a target value for the maximum force to reach during energy minimization. I don't know that there is a terribly scientific way to determine what it should be, except for NMA calculations where it is particularly important. The goal of EM is to achieve a reasonably stable system that is at an energy minimum and can be simulated further. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re, problem with EM
On 11/20/12 12:17 PM, Ali Alizadeh wrote: Dear Justin Thank you for your reply, 1- In the first plot, unit of y axis is kj/mol, and you said above i should use -nmol, i confused, Why is the unit of y axis kj/mol without using -nmol? Because that's the energy unit Gromacs always uses. The energy given is kJ per mole of equivalent systems. In the second plot shown above, the magnitude of the energy suggests kJ per mole of individual molecules. I understood, 2- I want do EM so that energy of my system reaches to considered value, but i never reach it exactly, what's wrong? You set an EM tolerance of 10 kJ/(mol-nm), which is a force, and mdrun achieved that. You can't ask an EM algorithm to produce the same result as a long-time MD run, as is shown above. -Justin That's right, I knew it but in your opinion, How can i get same result, What's the value of emtol for my system? If you want to reproduce the results of an MD trajectory, you need to be doing MD, not EM. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re, problem with EM
On 11/20/12 11:30 AM, Ali Alizadeh wrote: Dear All users I want my energy minimization of my system is converged to considered value, when i do it, It is converged because it reachs to Fmax and i see this message : Steepest Descents converged to Fmax < 10 in 31702 steps Potential Energy = -1.6531438e+03 Maximum force = 9.8014317e+00 on atom 162 Norm of force = 2.9060462e+00 my result: http://alichemical.persiangig.com/document/em.jpg When i represent profile of potential energy by g_energy, i can't see my considered results, I should reach this result that this link is related to it, http://alichemical.persiangig.com/document/11.jpg Justin wrote: The first plot shows the result of EM, the second is the result of a relatively long MD simulation. I would not expect them to show the same result. Further, it appears that the second plot pertains to the configurational energy per water molecule (based on magnitude), while the first simply measures the potential energy of the whole system. Since the system is homogeneous, you can use the -nmol option of g_energy to divide the energy terms by the number of molecules. -Justin Dear Justin Thank you for your reply, 1- In the first plot, unit of y axis is kj/mol, and you said above i should use -nmol, i confused, Why is the unit of y axis kj/mol without using -nmol? Because that's the energy unit Gromacs always uses. The energy given is kJ per mole of equivalent systems. In the second plot shown above, the magnitude of the energy suggests kJ per mole of individual molecules. 2- I want do EM so that energy of my system reaches to considered value, but i never reach it exactly, what's wrong? You set an EM tolerance of 10 kJ/(mol-nm), which is a force, and mdrun achieved that. You can't ask an EM algorithm to produce the same result as a long-time MD run, as is shown above. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
