Dear all, We have a 419 amino acid long protein and planned Protein-ligand complex MD simulation using Gromacs 5.1.4 to check.
1. What sought of MD simulation we have to perform?. 2. Restrain protein alone or Restrain both protein and ligand during simulation?. 3. What is the exact command for Drug positional RMSD plot? 4. What is the exact command for Number of Hydrogen bond plot? 5. What is the exact command for Other interactions between protein and ligand? 6. how to view the trajectory files? or We have to convert the frames to *.pdb and view in Pymol? Regards, Adarsh V. K. -- 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.
