[gmx-users] Visualize Protein ligand complex after simulation

Erik Marklund erikm at xray.bmc.uu.se
Mon Jan 28 15:42:47 CET 2013

Short answer is to inspect your complex with VMD or Pymol (or some  
other viewer). Pymol takes pdb input, so unless your structure is  
contained in a pdb file you must convert it with e.g. trjconv first.  
If you want a single frame you need to extract one form your  
trajectory, or, if the final frame form your simulation suffices, then  
use the -c output from mdrun. Most likely you will want to take care  
of the periodic boundary conditions, so a round of trjconv is probably  
needed anyway.

Ask again or look at the gromacs mailing-list archive if there is  
anything specific that puzzles you.


On Jan 28, 2013, at 3:30 PM, Sainitin Donakonda wrote:

> Hello,
> Recently i started working on molecular dynamics on my protein ligand
> complex using gromacs i successfully did simulation but i dont know   
> how to
> visualize this protein-ligand complex this after MD simulation
> Can any body tell me how to do it?
> Thanks
> Nitin
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