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

[Mark Abraham]

Hi,

Maybe they made a mistake.  You could try asking them, rather than some
strangers on the internet :-D

Mark

On Tue, Aug 11, 2015 at 5:53 AM dipak sanap <dipak94sanap at gmail.com> wrote:

> 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.
> > > --
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