[gmx-users] getting started with gromacs

kumud agarwal kumud0405 at gmail.com
Thu Jan 26 16:15:46 CET 2012


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?

Kumud Agarwal

On Tue, Jan 24, 2012 at 11:26 AM, Justin A. Lemkul <jalemkul at 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
> 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>
> ==============================**==========
> --
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