Thanks Justin, That is very helpful. I can run the water example provided in your paper with the GROMACS "drude" branch.
I have built my own tools to construct a core-shell MD topology file for my system. Grompp produces a tpr without complaint but mdrun crashes after the first step with a segmentation fault and no other useful errors. I am trying to troubleshoot. Is it required that each drude/shell immediately follow the atom it is attached to in the atoms directive and the input coordinate file? For convenience, I have attached them to the end of each molecule? In my topology, I manually account for the fact that drude/shell particles are attached with bonds which count when evaluating exclusions. Specifically, I assume a "3" in the molecules directive will take care of all exclusions up to 3 bonds away. To account for the extra bond lengths introduced by drude/shell particles, I add manually add certain exclusions for particles that should be 3 bonds away according to the atom-atom connectivity. Will this work or is there some "gotcha" I don't understand. For example, do you invalidate the moleculetype directive by providing an exclusions directive? Best, Eric On Tue, Jul 3, 2018 at 5:39 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/3/18 6:52 PM, Eric Smoll wrote: > >> Justin, >> >> Thanks again for the response and the guidance. Your 2015 JCC paper on >> the >> subject was very helpful. >> >> Your code uses a different thole_polarization format. Currently, Gromacs >> uses the following format >> [ thole_polarization ] >> ; i j k l function-number thole-a-parameter alpha_ij >> alpha_kl >> >> Your code seems to use >> [ thole_polarization ] >> ; i j k l function-number alpha_ij alpha_kl >> thole-a-parameter-1 thole-a-parameter-2 >> >> If I would use 2.6 in the current Gromacs thole_polarization format, what >> would I use in your thole_polarization format? >> > > 1.3 for both atoms to get 1.3 + 1.3 = 2.6. Thole's magic number quickly > breaks down for complicated molecules, so our convention is that it is a > per-atom value that is summed to give a new value of "a" per pair, e.g. a_i > + a_j = a_total. > > -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.