[gmx-users] the final structure

[Justin A. Lemkul]

ahmet yıldırım wrote:
> Dear users,
> 
> Which the file should I use to visualize (using pymol) the final 
> structure after the simulation finish?
> 

The final structure is contained in whatever file you specified with the mdrun 
-c flag.  By default, it is a .gro, which I don't believe PyMOL can handle, so 
you can convert it to a .pdb with editconf.  Or, if PyMOL is your preferred 
program, set a .pdb file to be your mdrun -c output.

-Justin

> Thanks
> 
> -- 
> Ahmet YILDIRIM
> 

-- 
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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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