[gmx-users] Increase Graphene sheet size

[Dallas Warren]

genconf will only stack the box that you have in the original box in
integer values.

i.e. -nbox 2 4 10

If want a specific dimension, then the box you are stacking has to be an
integer fraction of the final dimensions.

Also note that the final dimension also has to be possible with the
inter-atomic distances for the carbon atoms that make up the sheet.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Mon, 17 Feb 2020 at 21:11, 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.
>
> Thanks,
> Mohamed
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