Hi Alessandra, Many thanks again for your help :)
That sounds great. I can simulate a box with the desired dimensions. I repeated the graphene sheet using genconf into dimensions greater the desired dimensions and then I created a box with the desired dimensions and I solvate it to visualize it. now I have an additional part of the graphene sheet which is out of the box, How can I remove it. I want my simulation and visualization to be with a specific dimensions which is the dimensions of the box. I would appreciate if you can further clarify how can I do that. Thanks, Mohamed On Wed, Feb 19, 2020 at 10:10 Alessandra Villa < alessandra.villa.bio...@gmail.com> wrote: > HI, > > > > On Wed, Feb 19, 2020 at 10:31 AM Mohamed Abdelaal <m.b.abdel...@gmail.com> > wrote: > > > 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. > > > > > Yes/No, gmx solvate is normally used to add water or to build solvent box > but my suggestion was to use gmx solvate tools for your aim. > What I suggested was to use the tool to fill an empty box (of desidered > dimension) with copies of your graphene pre-equilibrated (small) sheet. > > Best regards > Alessandra > > > > 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. > > > -- > 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.