Many thanks Alessandra for your reply :) gmx solvate will add water around my graphene sheet but will not increase the graphene sheet itself. Please correct me if I am wrong.
I already simulated the graphene sheet but I need to increase its dimension to a certain dimensions. any Ideas how to do that :) ? Thanks, Mohamed On Tue, Feb 18, 2020 at 8:16 AM Alessandra Villa < alessandra.villa.bio...@gmail.com> wrote: > Hi > > On Mon, Feb 17, 2020 at 11:11 AM Mohamed Abdelaal <m.b.abdel...@gmail.com> > wrote: > > > Hello All, > > > > I want to create a graphene sheet with a specific dimensions > (10*15*0.284) > > nm. > > > > I created a .gro file as below ( as mentioned in this website > > > > > https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/ > > ) > > > > GRM: 1 1 Rcc=1.420 Rhole=0.000 Center: Ring > > 4 > > 1GRM C1 1 0.061 0.071 0.000 > > 1GRM C2 2 0.184 0.142 0.000 > > 1GRM C3 3 0.184 0.284 0.000 > > 1GRM C4 4 0.061 0.355 0.000 > > 0.245951 0.426000 0.284000 > > > > Now I don't know how to use genconf to repeat it until it gives me the > > required dimensions. As using genconf -nbox will repeat the above into a > > specific number of boxes but I can't get a sheet with accurate dimensions > > of (10*15*0.284 nm). > > > > I tried to generate a sheet using gencong and then use editconf to change > > the dimensions to the required ones, but the problem is that using > editconf > > will put the graphene sheet in an empty box but will not change the > > dimension as I want. > > > > Another option is to divide the 10 (the required dimension) nm by > 0.245951 > > (the dimension in the above .gro file) and to use the genconf with the > > result but it will be a lot of decimals and I am not sure if it will also > > give me the accurate dimension. > > > > Can anybody help me or guide me how to solve that problem. > > > > > you could try gmx solvate. It is not elegant solution but it may work, the > limitation is that you do not control on the orientation and other > geometrical parameter that may be relevant for graphene sheet. > > 1) generate an empty box with the desired dimension (empty.gro) > 2) run gmx solvate -cp empty.gro -cs small_graphene.gro ..... -o > > or in alternative you can use -cs and -box > for all the options see > > http://manual.gromacs.org/documentation/current/onlinehelp/gmx-solvate.html?highlight=gmx%20solvate > > Best regards > Alessandra > > > > 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.