Justin, In a previous thread on core/shell optimization ( https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-August/091101.html) you state:
"No, I've made wholesale changes to the code in the way that energies and forces are computed. The current code has bugs. If you want a modified version (beta software, so caveat emptor), contact me off-list." Is this still true? Is core/shell optimization broken in GROMACS 2018.1? If so, would you mind sharing your Drude implementation? Best, Eric On Mon, Jun 18, 2018 at 1:14 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/18/18 4:05 PM, Eric Smoll wrote: > >> Justin, >> >> Thank you so much for the rapid and clear reply! Sorry to ask for a bit >> more clarification. >> >> The thole_polarization isn't in the manual at all. Is it structured the >> same way as the [ polarization ] directive in the manual: >> >> [ thole_polarization ] >> ; Atom i j type alpha >> 1 2 1 0.001 >> >> If I want Thole corrections, am I correct in assuming that I should list >> *all shells* in the system under this thole_polarization directive with >> (as >> you pointed out) "i" or "j" as the shell? If "i" is the shell, "j" is the >> core. If "j" is the shell, "i" is the core. >> > > You have to list everything explicitly, including the shielding factor, > and between dipole pairs (Thole isn't between an atom and its shell, it's > between neighboring dipoles). I honestly don't know what the format is; I > completely re-wrote the Thole code for our Drude implementation (still not > officially incorporated into a release due to DD issues, but we're close to > a fix...) > > The code for "init_shell_flexcon" was very helpful. Thank you! >> nstcalcenergy must be set to 1. The code says that domain decomposition >> is not supported so multi-node MPI calculations are not allowed. I can >> still use an MPI-enabled GROMACS executable on a single node for shell MD, >> correct? Thread parallelization is still permitted, correct? >> > > Presumably you're limited to OpenMPI, but again I have no idea about this > code. I've never actually used it. > > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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. > -- 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.