Hi Ehud! Your settings are correct. However, you can also use domain decomposition with GB, and I at least usually bypass the editconf stage, and do pdb2gmx->grompp->mdrun, when you do not want any pbc.
/Per 7 okt 2010 kl. 12.29 skrev Ehud Schreiber: > Dear GROMACS users, > > I try to compute energies of a small peptide-domain complex and of its > constituents using implicit solvent, so that I can get the binding Delta E. I > need the accuracy to be high enough so that I can reliably measure the Delta > Delta E between the wildtype peptide and a mutation of it. > > I would like to get advice as to the best setting and parameters to use; are > the ones given below the correct and best ones (most in an mdp file, some run > control parameters of GROMACS commands)? Are other defaults in need to be > changed? > > As the GBSA method necessitates using the inexact cut-off interactions, and > my system is rather small, I consider using no cut-off at all, i.e. an > all-vs.-all approach. For that I understand the parameters should be > nstlist=0 > ns_type=simple > -pd ; in mdrun > coulombtype=cut-off > rcoulomb=0 > vdwtype=cut-off > rvdw=0 > rlist=0 > > Then, there are the implicit solvent parameters themselves: > implicit_solvent=GBSA > gb_algorithm= Still > sa_algorithm=Ace-approximation > rgbradii=0 > > Finally, regarding the simulation box, I see no need for periodic boundary > conditions, and I pick some big margin around the system (as there are no > water molecules, no need to spare): > pbc=no > -d 5.0 ; in editconf > > What do you say? > > Thanks, > Ehud. > -- > 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
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