I want to insert an atom with a velocity moving downwards toward the graphene sheet in my box. Yes I need to remove any atom moving away from my substrate or the deposited atoms and far by 0.4 nm. Then repeat the process until I have inserted 3000 atoms.
Thanks for your reply. Mohamed On Wed, Mar 11, 2020 at 13:43 John Whittaker < johnwhitt...@zedat.fu-berlin.de> wrote: > Write a script that calls gmx insert-molecules 3000 times and uses the > previous output as input for each call. > > > http://manual.gromacs.org/documentation/current/onlinehelp/gmx-insert-molecules.html > > Is there something you have to do in between each insertion? > > - John > > > Hello everybody, > > > > I am trying to insert molecules into a box but I have to insert one > single > > molecule at a time reaching 3000 molecule in total. Is there a way to > > automate this process ? > > > > Thanks > > Mohamed > > -- > > 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. > > > > > -- > 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. > -- 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.