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...@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 > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
