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<title>[gmx-users] Solvation Free Energy using PME</title>
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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hello I would like to calculate the
solvation free energy of ions. In order to do so I must use a switching
function or a reaction field. I would<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Prefer the switching function by I notice
that is very <span class=GramE>unstable<span style='mso-spacerun:yes'>
</span>when</span> I use it with the pressure coupling. Has anyone else noticed
this or used <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>The switching <span class=GramE>function</span>
and if so what were your parameters?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Thanks<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Ilya<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Tahoma><span
style='font-size:10.0pt;font-family:Tahoma'>-----Original Message-----<br>
<b><span style='font-weight:bold'>From:</span></b> gmx-users-admin@gromacs.org
[mailto:gmx-users-admin@gromacs.org] <b><span style='font-weight:bold'>On
Behalf Of </span></b>Nagy, Peter I.<br>
<b><span style='font-weight:bold'>Sent:</span></b> Tuesday, March 16, 2004 5:14
AM<br>
<b><span style='font-weight:bold'>To:</span></b> gmx-users@gromacs.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> RE: [gmx-users] Solvation
Free Energy using PME</span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText style='margin-left:.5in'><font size=2 face="Courier New"><span
style='font-size:10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText style='margin-left:.5in'><font size=2 face="Courier New"><span
style='font-size:10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText style='margin-left:.5in'><font size=2 face="Courier New"><span
style='font-size:10.0pt'>----------------------------------------------------------------------------------------------<o:p></o:p></span></font></p>
<p class=MsoPlainText style='margin-left:.5in'><font size=2 face="Courier New"><span
style='font-size:10.0pt'>Dr. Ilya Chorny<span
style='mso-spacerun:yes'>
</span>Department of Pharmaceutical Chemistry<o:p></o:p></span></font></p>
<p class=MsoPlainText style='margin-left:.5in'><font size=2 face="Courier New"><span
style='font-size:10.0pt'>DOE/SLOAN Postdoctoral Researcher<span
style='mso-spacerun:yes'> </span>University
of California, San Francisco<o:p></o:p></span></font></p>
<p class=MsoPlainText style='margin-left:.5in'><font size=2 face="Courier New"><span
style='font-size:10.0pt'>Tel:<span style='mso-spacerun:yes'>
</span>(415)-476-6875<span
style='mso-spacerun:yes'>
</span>600 16th st<o:p></o:p></span></font></p>
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</span>(415)502-4222<span
style='mso-spacerun:yes'>
</span>San Francisco, CA 94107<o:p></o:p></span></font></p>
<p class=MsoPlainText style='margin-left:.5in'><font size=2 face="Courier New"><span
style='font-size:10.0pt'>Cell: (408)887-8496<o:p></o:p></span></font></p>
<p class=MsoPlainText style='margin-left:.5in'><font size=2 face="Courier New"><span
style='font-size:10.0pt'><span
style='mso-spacerun:yes'>
</span>Email: ichorny@maxwell.ucsf.edu<o:p></o:p></span></font></p>
<p class=MsoPlainText style='margin-left:.5in'><font size=2 face="Courier New"><span
style='font-size:10.0pt'>----------------------------------------------------------------------------------------------<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> I think that this is an
interesting problem. I am not an experienced GROMACS user, and my remark would
rather refer to a more thereoretical point. The question depends on the
definition of the solvation free energy. <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> If you want to see the free
energy difference between a gaseous and an in-solution anion, then I think NO
counterion should be added to the solution model. I presume that the free
energy calculation would be performed by annihilation of the anion in the solvent.
If the counterion is present then the anion-cation interaction will be ceased,
which would have a large effect on the calculated value.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> The corresponding physical
procedure would be that the anion is being formed in the gas phase
and enters the solvent without grabbing a cation, also
necessarily encountering in the gas phase. This is difficult to
perform technically, and I believe that the experimental values are determined
by indirect procedures. You may want to consult the paper of Pearson (J.Am.Chem.
Soc., 1986, 108, 6109) and that of Rossinsky (Chem. Rev., 1965, 65, 467). <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> So I think that no counterion
should be considered. In this case, the Ewald in GROMACS may not work
properly. But since a single anion in a solvent is not a real physical system
(except under very special technical conditions), if one uses Ewald one would
calculate anion-anion repulsive interactions without considering anion-cation
attractive interactions, generally present for a real system.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> For such a case, Jorgensen et al. (Chem.
Phys., 1989, 129,193) used a cutoff and the Born approximation in Monte Carlo
simulations. The Born radius was set to the cutoff. Good result was obtained<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>for the chloride anion.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>in a dielectric with<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Peter Nagy<o:p></o:p></span></font></p>
</div>
<blockquote style='margin-top:5.0pt;margin-right:0in;margin-bottom:5.0pt'>
<div>
<p class=MsoNormal style='mso-margin-top-alt:0in;margin-right:0in;margin-bottom:
12.0pt;margin-left:.5in'><font size=2 face="Times New Roman"><span
style='font-size:10.0pt'>-----Original Message----- <br>
<b><span style='font-weight:bold'>From:</span></b>
gmx-users-admin@gromacs.org on behalf of Ilya Chorny <br>
<b><span style='font-weight:bold'>Sent:</span></b> Tue 3/16/2004 3:02 AM <br>
<b><span style='font-weight:bold'>To:</span></b> gmx-users@gromacs.org <br>
<b><span style='font-weight:bold'>Cc:</span></b> <br>
<b><span style='font-weight:bold'>Subject:</span></b> [gmx-users] Solvation
Free Energy using PME</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal style='mso-margin-top-alt:0in;margin-right:0in;margin-bottom:
12.0pt;margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p style='margin-left:.5in'><font size=2 face="Times New Roman"><span
style='font-size:10.0pt'>I would like to calc the solvation free energy of a
negative ion in water<br>
using perturbation.<br>
Is it possible using PME. If I include a counter ion it will contribute to<br>
the solvation free energy?<br>
Could I use a reaction field instead of PME(how different will my results<br>
be?). I tried the switching<br>
function for my long range forces but I have been experiencing instability<br>
using the switching<br>
function. Any recomendations would be greatly apprecited.<br>
<br>
Thanks<br>
<br>
Ilya<br>
<br>
<br>
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