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

--
========================================

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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