By setting the emtol to 1.0, didnt work. Anyother way i could figure out. On Thu, Feb 9, 2012 at 6:32 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > lina wrote: > >> On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar <aiswarya.pa...@gmail.com> >> wrote: >> >>> Dear Gromacs users, >>> >>> I have a MD simulated protein and i take frame from this and remove water >>> and add water implicit in the interface and want to do energy >>> minimization >>> but while doing the minimization i get errors. The steps followed are- >>> >>> pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap >>> grompp -f minim.mdp -c 1oco.pdb -p 1oco.top -o 1oco.tpr >>> >>> The minim.mdp file = >>> >>> ; Lines starting with ';' ARE COMMENTS >>> ; Everything following ';' is also comment >>> >>> title = Energy Minimization ; Title of run >>> >>> ; The following line tell the program the standard locations where to >>> find >>> certain files >>> cpp = /lib/cpp ; Preprocessor >>> >>> ; Define can be used to control processes >>> define = -DFLEXIBLE >>> >>> ; Parameters describing what to do, when to stop and what to save >>> integrator = steep ; Algorithm (steep = steepest descent >>> minimization) >>> emtol = 1000.0 ; Stop minimization when the maximum force < 1.0 >>> >> emtol = 1.0 >> > > If mdrun could not converge to 1000, setting a target of 1 will not solve > anything. The OP should refer to: > > 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<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> > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore
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