On Thu, 2 Jun 2016 08:27:15 +0000 "Nash, Anthony" <a.n...@ucl.ac.uk> wrote:
> Dear Hannes, > > Thanks for all the help yesterday, it helped. I, hopefully, have just > the one final question. > > I am still a little confused how Gromacs deals with the interactions > (vdW & Coul) with the environment when a soft-core potential has been > used to switch between molecules (typeA and typeB in the topology > file). I understand how lambda can be used to 1) phase out the charge > then 2) phase out the vdW interactions for a molecule that is > disappearing (or reverse for appearing) to capture hydration > energetics e.g., Justin¹s methane in water FE tutorial. > > However, in the case of a D2K (aspartic-acid to lysine) > dual-topology How is your setup dual-topolgy? http://dx.doi.org/10.1002/jcc.23804 indicates to me that the pmx approach seems to go for as much single topology as possible. Your case seems to fall into this particular category. > how are the vdW and charges brought back into play for > typeB, when the interactions of typeA have been coupled to lambda as > per your example below? In a second setup as explained earlier, assuming you want to separate vdW from Coulomb. See attachment for an unrelated example system. -- 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.
