hi I followed the tutorial "lysozyme in water"
I have done upto energy minimization step i.e. mdrun -v -deffnm em I have the em.gro file Do I need to follow the next steps - equilibration, production MD and analysis because I just wanted to do the energy minimization of my initial peptide structure? Also is it possible to convert em.gro file into a pdb file? Thanks Kumud Agarwal On Tue, Jan 24, 2012 at 11:26 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > kumud agarwal wrote: > >> I want to do energy minimization of a small peptide (19 residues long) >> file (in pdb format). >> >> Can you please tell which tutorial is best for this purpose and which >> force field should I use. >> >> > Any of these should be fine: > > http://www.gromacs.org/**Documentation/Tutorials#**General_GROMACS_Use<http://www.gromacs.org/Documentation/Tutorials#General_GROMACS_Use> > > As for the force field, there is no single "best" option. Each force > field has its own sucesses and failures. You should plan to invest > significant time learning about each of the force fields and deciding which > is best for your application, based on known limitations and the underlying > theoretical basis for it. Choosing a force field is one of the most > significant steps in conducting a quality simulation. > > > -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> >
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