[gmx-users] convergence problem
Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. Output of energy minimization step is like this. Reached the maximum number of steps before reaching Fmax 100 writing lowest energy coordinates. Steepest Descents did not converge to Fmax 100 in 20001 steps. Potential Energy = -2.3055431e+05 Maximum force = 4.9160068e+02 on atom 3105 Norm of force = 8.8015385e+00 Is it wrong to do equilibration step further? and how to converge energy here? -- 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] convergence problem
On 11/28/12 4:20 AM, Shine A wrote: Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. Output of energy minimization step is like this. Reached the maximum number of steps before reaching Fmax 100 writing lowest energy coordinates. Steepest Descents did not converge to Fmax 100 in 20001 steps. Potential Energy = -2.3055431e+05 Maximum force = 4.9160068e+02 on atom 3105 Norm of force = 8.8015385e+00 Is it wrong to do equilibration step further? and how to converge energy here? I've never reached an Fmax 100 for a membrane protein system. Likely your result is stable enough to proceed. -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
[gmx-users] convergence
Hi all I have generated a PMF curve over 15 ns. Does g_wham have a facility whereby I can calculate the PMF over say 7 ns, to check for convergence. There doesn't seem to be anything in the manual. Many thanks Gavin -- 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
