[gmx-users] Protein-ligand interaction analysis after MD simulation

[Smith, Micholas D.]

If you just want to watch a "pretty" video of the simulation, you could used the VMD package (just a quick duckduckgo search away) or the Avogadro package. You should note that before viewing the simulation in VMD it is best if you do some post-processing to center and wrap your system so that the visual doesn't have the protein/lignin complex looping across any periodic boundaries.


===================
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of salam pradeep <salampradeep at gmail.com>
Sent: Thursday, March 26, 2015 8:35 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Protein-ligand interaction analysis after MD simulation

Dar Gmx Users,

I have performed 20ns protein-ligand complex md simulation. Now, pl let me
know how to visualize the 2D or 3D protein-ligand interaction after the 20
ns md simulation.


Yours sincerely
Salam Pradeep
Tezpur University, Assam, India
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