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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