<HTML dir=ltr><HEAD><TITLE>[gmx-users] Concentration of Urea in urea solvation box</TITLE>
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<DIV dir=ltr><FONT face=Arial color=#000000 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>
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<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> gmx-users-bounces@gromacs.org on behalf of mon_sharma@research.iiit.ac.in<BR><B>Sent:</B> Thu 9/4/2008 2:51 PM<BR><B>To:</B> gmx-users@gromacs.org<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 gmx-users@gromacs.org<BR><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please search the archive at <A href="http://www.gromacs.org/search">http://www.gromacs.org/search</A> before posting!<BR>Please don't post (un)subscribe requests to the list. Use the<BR>www interface or send it to gmx-users-request@gromacs.org.<BR>Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A><BR></FONT></P></DIV></BODY></HTML>