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

dipak sanap dipak94sanap at gmail.com
Sun Aug 9 07:36:27 CEST 2015

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.


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