[gmx-users] Increase Graphene sheet size

[Mohamed Abdelaal]

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.biosim at gmail.com> wrote:

> Hi
>
> On Mon, Feb 17, 2020 at 11:11 AM Mohamed Abdelaal <m.b.abdelaal at 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
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