for EM you can probably ignore this, but note that these are the wrong cutoffs for CHARMM27. (rlist=1.2 rlistlong=1.4 rcoulomb=1.2 rvdw=1.2 rvdw_switch=0.8 and vdwtype=switch).
On 2012-09-19 11:04:47AM +0100, Lara Bunte wrote: > 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 -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- 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
