I think your original problem is that you define only one charge group for the entire molecule/polymer. You need to define each bead in a separate charge group and things will be fine :)) you do not have charges anyways.
As far as I know angles have never made martini unstable but the conventional dihedral potential are not suited for martini or any flexible molecule. XAvier. On Jan 2, 2013, at 4:55, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/1/13 10:51 PM, Xu Dong Huang wrote: >> @Justin, >> >> Does the philosophy described in your tutorial apply to CG martini bead >> models where 1 bead describes the entire CO2 atom? (If I were to do that, >> assuming) > > Presumably. As long as you satisfy the criteria mentioned in the tutorial > (moment of inertia and total mass), you should be able to get it to work. > I've never dealt with polymers and have very little personal experience with > CG models, so I don't know if there are other methodological issues that one > might encounter. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 -- 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
