Re: [gmx-users] question to mdp file
On 7/3/12 8:25 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Ah okey. Yes sorry that was a typo...I ment nsteps. So but is there a possibility to define a minimal step size so that the minimization ends when the energy does not changes much any more? Just set emtol to some unreasonably low value, and mdrun will end with this message (which is not really an error): http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision You can set emstep to whatever size you like to reach this point. -Justin On 7/3/12 8:11 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, is it correct when I set the nstep = -1 and emtol = $number that the minimization goes as long as the energy difference between the previous step and this step is not lower as $number. And that there is no maximal stepsize? No. The value of emtol is the target for the maximum force to define convergence, not the difference between previous and current steps, and it's not an energy term, it's force. The maximum step size is always set in emstep. What's more, "nstep" is not a correct keyword, but "nsteps" is. -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 * Only plain text messages are allowed! * 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 -- 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 * Only plain text messages are allowed! * 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] question to mdp file
Ah okey. Yes sorry that was a typo...I ment nsteps. So but is there a possibility to define a minimal step size so that the minimization ends when the energy does not changes much any more? > > > On 7/3/12 8:11 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi everybody, >> is it correct when I set the >> nstep = -1 and >> emtol = $number >> >> that the minimization goes as long as the energy difference between the >> previous step and this step is not lower as $number. And that there is >> no >> maximal stepsize? >> > > No. The value of emtol is the target for the maximum force to define > convergence, not the difference between previous and current steps, and > it's not > an energy term, it's force. The maximum step size is always set in > emstep. > What's more, "nstep" is not a correct keyword, but "nsteps" is. > > -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 > * Only plain text messages are allowed! > * 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] question to mdp file
On 7/3/12 8:11 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, is it correct when I set the nstep = -1 and emtol = $number that the minimization goes as long as the energy difference between the previous step and this step is not lower as $number. And that there is no maximal stepsize? No. The value of emtol is the target for the maximum force to define convergence, not the difference between previous and current steps, and it's not an energy term, it's force. The maximum step size is always set in emstep. What's more, "nstep" is not a correct keyword, but "nsteps" is. -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 * Only plain text messages are allowed! * 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
