Dear Gromacs users, I've performed a membrane-protein simulation by charmm36ff as described below: 1. 10ns of NVT equilibration with position restrained on the protein 2. 50ns of NPT equilibration with position restrained on the protein 3. 200ns of NPT equilibration without position restrained on the protein Now I would like to calculate analyzes to ensure the stability and the convergence of the simulation. So, my questions are:
1. Which analysis should I calculate? except for RMSD, the area per lipid, bilayer-thickness, and temperature, pressure, total-energy, dimensions size convergence? 2. I divided the equilibration into three parts as described above, should I concatenate the .edr files from the *whole simulation* to make the fixed.edr file (meaning from the beginning till the end (from NVT to NPT_without restrains) in order to create the xvg files? 3. Following the equilibration of the whole system, I would like to run the simulation itself. I'm working on a dimer (amyloid)-membrane system and I'm interested in the interactions between the two attached monomers and the membrane. Now my question is should I release the H-bond constraints in the production step? and if so, what should I put at the constraints category at the mdp file? in this step I will not use the position restrains but what about the H-bond constraints? Thanks in advance Olga -- 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.