Hello I want to do md simulations with the amino acid alanin for practice. I choose alanin because it is parametrized in my forcefield. I use charmm27.
I created with pdb2gmx my topology and I use water model tip3p. I choosed a dodecahedron box with distance of 0.5 between the solute and this box. With genbox and the solvation I used spc216 model. Next I want to run an energy minimization and I create this em.mdp file: integrator = steep emtol = 1000.0 emstep = 0.01 nsteps = 5000 nstlist = 1 rlist = 0.7 coulombtype = PME rcoulomb = 0.7 vdw-type = cut-off rvdw = 0.7 nstenergy = 10 grompp works but I got this note: NOTE 1 [file em.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing Is this necessary for me to increase cut-off and PME grid spacing or can I ignore this note? I would be thankful if you could explain that to me. Thanks for help Greetings Lara -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
