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

[dipak sanap]

Hi all,

Thank you very much for your reply Mark, Still if i see little variation of
few molecules here and there as explained in my original post, should I go
ahead with it ?
I am requesting again, can someone please tell me which method people
usually follow?

On Sun, Aug 9, 2015 at 11:04 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>