[gmx-users] Concentration of Urea in urea solvation box

[Anil Kumar]

As Peter has said you have to maintain the ratio of water molecule with
respect to urea to get the desired concentration.

So, in your case your system must have ratio of Water:Urea = 6.9375:1 (what
i understood from the logic of calculation) for 8m Urea concentration (Plz
note urea concentration is usually taken in molal not in molar..be careful!)

You can start with the default urea+h2o.gro file of gromacs which has
concentration of 6m...and do some editing according to your desired
concentration followed by density adjustment and equilibrate it for sometime
thats it.

with regards
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On Fri, Sep 5, 2008 at 1:23 AM, Nagy, Peter I. <PNAGY at utnet.utoledo.edu>wrote:

>  Without an experiment you may not know the correct composition. 1 dm3
> water contains 55.5 mol water. If you
> want to model a 8M urea solution, you should replace the correct number of
> the water molecules / 55.5 water.
> An urea (H2NCONH2 if I am not mistaken) contains 4 heavy atom. If you
> replace 8x4 water molecules by 8 urea in
> every 55.5 water subsystem, then you will have a good starting point. Then
> run an NpT job and check the volume.
> For example, if you start with 555 water molecules, replace 320 of them by
> 80 urea and so on. After an equilibration
> phase (1 ns or so) you will find a stable density, and see whether the
> density corresponds to 8M urea / 1dm3. Then
> you can make an estimate, how to modify the composition if necessary
> because of the too low or high concentration
>
> Peter Nagy
> University of Toledo
>
> ------------------------------
> *From:* gmx-users-bounces at gromacs.org on behalf of
> mon_sharma at research.iiit.ac.in
> *Sent:* Thu 9/4/2008 2:51 PM
> *To:* gmx-users at gromacs.org
> *Subject:* [gmx-users] Concentration of Urea in urea solvation box
>
>  Hi All,
> This is a trivial question. But I am quite puzzled about it, and I
> really need someone's kind help.
>
> I want to prepare 8M urea solution box,
> for which I might need to know input as number of water molecules and of
> urea. Now my query is how to make sure of these exact number of molecules.
> I know its really a basic question. One thing could be by experiment if we
> can make sure exact
> number of moles of water added to make molar solution. But i dont have any
> access to such wet lab things. So if anyone can help me out how to do
> these back end calculations.
> Another query is will the box size also play a role?
>
> Please be patient with this trivial query, but this simple
> calculation question is baffling me from quite a few days.
>
> Thanks in advance,
> Regards,
> Monika
>
>
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