On Tue, 4 Oct 2016 13:08:51 +0300 Vlad <vlad_bal...@mail.ru> wrote: > It appears in the step where ligand starts to recouple (I start > from the decoupled ligand and consequently turn on vdw and then > charges). And the dG between the zero and the first init_lambda > appears about 1800 kJ/mol
Is there any particular reason why you cannot run a decoupling simulation? Creating a molecule out of "nothing" will need to push existing atoms aside and I can see why that could be a problem. Have you checked the trajectory to see what is happening? Cheers, Hannes. -- 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.
