Hi Justin, Using your code to generate the topology for my system still results in the distortion of bonds to hydrogen when constraints=h-bonds and emtol=100 (note that the energy minimization mdp files provided with your paper use an emtol of 1000). However, when I set constraints=none and emtol=100, no distortion of bonds to hydrogen occur. Maybe there is some problem using shells with constraints.
I am going to remove all constraints from my system and check if my system is stable with SCF and Lagrangian core-shell molecular dynamics. Best, Eric On Fri, Jul 13, 2018 at 6:14 PM, Eric Smoll <ericsm...@gmail.com> wrote: > Justin, > > Your pdb2gmx appears to exclude all intermolecular interactions for a > molecule with no hydrogen atoms. For instance, for a molecule with "N" > atoms indexed from "1" to "N," the first line of the generated exclusions > directive has a record with the "1 2 3...N" series. > > Is this expected? Shouldn't intramolecular nonbonded interactions be > permitted at and beyond 1-4 interactions? > > Best, > Eric > > On Fri, Jul 13, 2018 at 3:02 PM, Eric Smoll <ericsm...@gmail.com> wrote: > >> Hi Justin, >> >> Very grateful for the rapid reply and warning. If you suggest that I >> should tread lightly with polarizable H atoms, I will avoid it altogether. >> >> I will alter my troubleshooting plan and focus on using your edited >> pdb2gmx program (adding to the rtp, of course) to build a core-shell MD >> topology for my problem molecules. It should be easy to compare with the >> topology I have prepared with my own tools. They should be identical. >> >> Best, >> Eric >> >> On Fri, Jul 13, 2018 at 2:51 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >>> >>> >>> On 7/13/18 4:48 PM, Eric Smoll wrote: >>> >>>> Hello Justin, >>>> >>>> Thank you for the guidance. >>>> >>>> Although more testing is needed, molecules where shells are attached to >>>> every atom appear to be working properly. >>>> >>>> The issue appears to be with models where shells are only attached to >>>> heavy >>>> atoms and bonds between hydrogen atoms and heavy atoms are constrained. >>>> Initial energy minimization tests (emtol = 100) show that bonds between >>>> heavy atoms and hydrogen in organic molecules slowly stretch or compress >>>> far more than they should while the network of non-hydrogen atoms >>>> maintains >>>> a sensible geometry. All atom-drude displacements on the heavy atoms >>>> converge quickly and are stable. >>>> >>>> I am still hunting for whatever topology problem is causing this. All >>>> exclusions out to 1-4 interactions between atoms and drudes should be >>>> properly included (combined action of the moleculetype directive and >>>> additional exclusions directives). Thole screening only applies to >>>> atom-shell pairs so no screening is needed for 1-2 and 1-3 pairs with H >>>> atoms (no attached shells). It may be difficult to provide any useful >>>> guidance without details but troubleshooting suggestions are welcome if >>>> you >>>> have any. >>>> >>>> Are there issues associated with adding shells to specific atoms in a >>>> molecule? Are simulations that place shells on all atoms (hydrogen and >>>> heavy) more stable for some reason? I am going to build a new model >>>> where >>>> shells are attached to all atoms to see if bonds to hydrogen atoms still >>>> slowly compress/stretch during a tight-emtol energy minimization. >>>> >>> >>> I have never tested a system like that. Our Drude convention does >>> exactly what you seem to find a problem - Drudes on heavy atoms and not H, >>> with bonds to H constrained. I've never had the issue you're experiencing. >>> Without a full test case of complete inputs, I can't tell you anything. >>> >>> Be forewarned - I know of no efforts by me or anyone else to deal with >>> polarizable H atoms in GROMACS, and that may conflict with constraints, so >>> tread lightly... >>> >>> -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.