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

Nagy, Peter I. PNAGY at UTNet.UToledo.Edu
Thu Sep 4 21:53:33 CEST 2008

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,

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