[gmx-users] the final structure

Justin A. Lemkul jalemkul at vt.edu
Wed Jan 19 14:06:40 CET 2011

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.


> Thanks
> -- 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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