Dear gmx users I’m in the process of creating a PE polymer surface.
pdb and itp files were obtained from ATB and were used to produce a (xyz) 142 x 6 x 60 A box ( starting size ) with 300 150 A long molecules. They were neatly aligned to start and - using pcoupletype = surface-tension and a restraint on the x direction ( fc=10) they stay aligned through md but are now in bundles - which is what they should do But now I want to compress ( move them in the y direction ) the bundles into a 142 x 6 x say 20 A box. i.e. a more or less complete surface I’ve tried re-running npt on the first md result, with no change. (10 ns md) Making a smaller box ( smaller y) with confedit and running npt or md leads to very High PE. Other than waiting for the cows to come home using md,, could a suggestion be made to coerce the bundles to come together ? regards Paul -- 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.
