# [gmx-users] Preparation of simulation system for GdmCl and protein simulation.

Mark Abraham mark.j.abraham at gmail.com
Sun Aug 9 19:34:16 CEST 2015

```Hi,

As you have seen, if you have a periodic simulation volume dominated by
e.g. protein then the standard definition of concentration will not lead to
conditions analogous to e.g. an experiment with protein in a bulk solution.
Choose something that models the relevant aspects well, defend it with a
reason, and you'll be fine.

Mark

On Sun, 9 Aug 2015 07:36 dipak sanap <dipak94sanap at gmail.com> wrote:

> Hi all,
>
> I am neophyte at GROMACS. I have a very basic question regarding
> preparation of simulation box of specified molar conc.of GdmCl.
>
> Lets say, I need to make 2 M GdmCl solution. That means 2
> moles=2*6.022*10^23 molecules in a liter [10^(-3) m^3] solution (Assumption
> :Density is 1000kg/m^3) .And I know the V [(31.255875*10(-27) m^3] of
> simulation box. (I first insert one GdmCl molecule in pre-specified cubic
> box of 3.15 nm side and the rest of the molecules using genbox).
> So, 2*6.022*10^23/10=N/V . where N is number of GdmCl required which is 38
> by my calculation. However, in one published article (
> http://dx.doi.org/10.1103/PhysRevE.88.052708) this number is 42.  FYI i am
> trying to replicate these results for some reason.
>
> My another approach involves mole fraction calculation. Assuming in all
> GdmCl solutions, moles of water will be same irrespective of volume of the
> solution. i.e. 1L=1000g=55.55 moles of water. I calculate mole fraction of
> GdmCl =2/57.55=0.03475238922 but in article cited above for 2M solution
> they have 42 GdmCl molecules in 870 molecules of water which gives GdmCl
> mole fraction (42/(42+870))=0.04605263157. This is more confusing to me.
> And also after inserting 42 Gdm molecules, genbox is not able to fit
> (870+42=912) water molecules as after inserting Gdm I need to add same
> number of Cl ions(will be replaced by water molecules hence more 42 waters)
> to make whole GdmCl.In many different articles I see these variations, I am
> not able to find out the relevant method for these calculations.
>
> This will be even more complex when I introduce my protein (1IV7,what about
> volume of protein ?) in dodecahedron box( more complex box shape) with
> GdmCl and water. In conclusion, can someone edify me about how to choose
> box size and calculations to make a box of required concentration for these
> kind of simulations. Any help is appreciated, thank you very much.
>
> Regards,
> Dipak
> JRF, NCBS.
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