Dear all, Using the flat-bottom (K=4184 KJ/(mol. nm^2)) restrain I tried to have a smaller cubic box as semi-preamble walls inside a bigger cubic box so that all molecules except water would stay inside the smaller box during the simulation, however, the wall doesn't work and the molecules are also out of the smaller box in several replica's simulations each with 100 ns. The only reason I can imagine is that the K=4184 KJ/(mol. nm^2 is probably too low to keep the molecules inside the smaller box! I wonder if you know any other potential reason? how can I find out the reason?
Regards, Alex P.S. I am sure that I am using the flat-bottom restrain correctly as the same approach worked for some other systems of mine previously. -- 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.