[gmx-users] Protein+ligand complex

[Kashif]

Greetings of the day,
Can I use nvt.mdp and npt.mdp parameter file given in tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/index.html)
 for my 5 ns production run? As the tutorial shows 100 ps nvt and npt
equilibration and 1000 ps (1 ns) MD Simulation run. Which parameter should
be changed if there is any problem.

What are the post-simulation analysis commands used for the analysis for
protein+drug complex?


regards
Kashif