[gmx-users] Protein+ligand complex

[Kashif]

I have done MD simulation of my protein and ligand docked complex. My
protein is having 900 amino acids. When I use g_rms to analyse rmsd, the
graph is too short. Currently I am simulating my protein for 5 ns. Should I
increase my ns for such big protein and ligand complex?

On Tue, May 12, 2015 at 4:41 AM, Kashif <kashifzamir180.mk at gmail.com> wrote:

> 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
>