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.
Erik
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
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
