[gmx-users] getting started with gromacs

[Justin A. Lemkul]

kumud agarwal wrote:
> 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?
> 

If your purpose is EM, then you can stop.  The tutorial assumes the user wants 
to conduct a full MD simulation.

> Also is it possible to convert em.gro file into a pdb file? 
> 

Yes. Use editconf.

-Justin

-- 
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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

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