<div dir="ltr">As Peter has said you have to maintain the ratio of water molecule with respect to urea to get the desired concentration.<br><br>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!)<br>
<br>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.<br>
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---------------------------------------------------------------------------<br><br><div class="gmail_quote">On Fri, Sep 5, 2008 at 1:23 AM, Nagy, Peter I. <span dir="ltr"><<a href="mailto:PNAGY@utnet.utoledo.edu">PNAGY@utnet.utoledo.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<div dir="ltr"><font color="#000000" face="Arial" size="2">Without an experiment you may not know the correct composition. 1 dm3 water contains 55.5 mol water. If you </font></div>
<div dir="ltr"><font face="Arial" size="2">want to model a 8M urea solution, you should replace the correct number of the water molecules / 55.5 water.</font></div>
<div dir="ltr"><font face="Arial" size="2">An urea (H2NCONH2 if I am not mistaken) contains 4 heavy atom. If you replace 8x4 water molecules by 8 urea in </font></div>
<div dir="ltr"><font face="Arial" size="2">every 55.5 water subsystem, then you will have a good starting point. Then run an NpT job and check the volume.</font></div>
<div dir="ltr"><font face="Arial" size="2">For example, if you start with 555 water molecules, replace 320 of them by 80 urea and so on. After an equilibration</font></div>
<div dir="ltr"><font face="Arial" size="2">phase (1 ns or so) you will find a stable density, and see whether the density corresponds to 8M urea / 1dm3. Then </font></div>
<div dir="ltr"><font face="Arial" size="2">you can make an estimate, how to modify the composition if necessary because of the too low or high concentration</font></div>
<div dir="ltr"><font face="Arial" size="2"></font> </div>
<div dir="ltr"><font face="Arial" size="2">Peter Nagy</font></div>
<div dir="ltr"><font face="Arial" size="2">University of Toledo</font></div></div>
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<font face="Tahoma" size="2"><b>From:</b> <a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a> on behalf of <a href="mailto:mon_sharma@research.iiit.ac.in" target="_blank">mon_sharma@research.iiit.ac.in</a><br>
<b>Sent:</b> Thu 9/4/2008 2:51 PM<br><b>To:</b> <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><b>Subject:</b> [gmx-users] Concentration of Urea in urea solvation box<br></font><br></div>
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<p><font size="2">Hi All,<br>This is a trivial question. But I am quite puzzled about it, and I<br>really need someone's kind help.<br><br>I want to prepare 8M urea solution box,<br>for which I might need to know input as number of water molecules and of<br>
urea. Now my query is how to make sure of these exact number of molecules.<br>I know its really a basic question. One thing could be by experiment if we can make sure exact<br>number of moles of water added to make molar solution. But i dont have any<br>
access to such wet lab things. So if anyone can help me out how to do<br>these back end calculations.<br>Another query is will the box size also play a role?<br><br>Please be patient with this trivial query, but this simple<br>
calculation question is baffling me from quite a few days.<br><br>Thanks in advance,<br>Regards,<br>Monika<br><br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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