[gmx-users] Increase Graphene sheet size

[Mohamed Abdelaal]

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.biosim at gmail.com> wrote:

> HI,
>
>
>
> On Wed, Feb 19, 2020 at 10:31 AM Mohamed Abdelaal <m.b.abdelaal at 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.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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