Hello I read the mdp options more than once but I don't understand how to make a good em.mdp file for the first energy minimization, if you plug your molecule in a water box. In my tutorial is this example given.
integrator = steep nsteps = 200 nstlist = 10 rlist = 1.0 coulombtype = pme rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 nstenergy = 10 1.) Is it possible to use this as a standard for all first energy minimization. 2.) Is the choose of parameters here dependent on the force field? I use a CHARMM27, do you think I should change something? 3.) What are the criteria to choose these parameters? As I said I read the mdp options, so I know what this Option above mean, but I don't know how to know that this are the right parameters? To say my question in other words: How do I know how the em.mdp file has to look like? Thanks for helping me. Greetings Lara -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
