[gmx-users] Increase Graphene sheet size

[Alessandra Villa]

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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