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I guess the ionic strength is solution (0.1-0.15M) would do it. As the
number of ions near the protein surface changes during the simulation,
I don't think you can say much about the ionic strength near the
protein.<br>
<br>
Ran.<br>
<br>
Samuel C Flores wrote:
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<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;">Hmm..<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;">Well
counting the charged residues leads
to scores of ions, which I think would be a tight squeeze in my water
box,
given that each ion should have a hydration shell around it. <o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;">I like the
idea of neutralizing, then
adding ions to reach a certain ionic strength. However how to know
exactly what ionic strength I need? I am modeling murA, but haven’t
found an ionic strength in the literature. Also, wouldn’t the ionic
strength near the protein be different from that elsewhere in the
solution?
<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;">Sam<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;"><o:p> </o:p></span></font></p>
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<p class="MsoNormal"><b><font color="black" face="Tahoma" size="2"><span
style="font-size: 10pt; font-family: Tahoma; color: windowtext; font-weight: bold;">From:</span></font></b><font
color="black" face="Tahoma" size="2"><span
style="font-size: 10pt; font-family: Tahoma; color: windowtext;">
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>
[<a class="moz-txt-link-freetext" href="mailto:gmx-users-bounces@gromacs.org">mailto:gmx-users-bounces@gromacs.org</a>] <b><span
style="font-weight: bold;">On
Behalf Of </span></b>Ran Friedman<br>
<b><span style="font-weight: bold;">Sent:</span></b> Sunday, July 16,
2006 12:57
PM<br>
<b><span style="font-weight: bold;">To:</span></b> <st1:PersonName
w:st="on">Discussion list for GROMACS users</st1:PersonName><br>
<b><span style="font-weight: bold;">Subject:</span></b> Re:
[gmx-users]
counterions?</span></font><font color="black"><span
style="color: windowtext;"><o:p></o:p></span></font></p>
</div>
<p class="MsoNormal"><font color="black" face="Times New Roman"
size="3"><span style="font-size: 12pt;"><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="margin-bottom: 12pt;"><font color="black"
face="Times New Roman" size="3"><span style="font-size: 12pt;">Hi,<o:p></o:p></span></font></p>
<div>
<div>
<p class="MsoNormal"><font color="black" face="Times New Roman"
size="3"><span style="font-size: 12pt;">If you want to add ions near
charged residues and want
to know how much, just count the number of charged residues, and add
one
positive and one negative charge for the N- and C- termini.<o:p></o:p></span></font></p>
</div>
<p class="MsoNormal"><font color="black" face="Times New Roman"
size="3"><span style="font-size: 12pt;">You can use g_sas to locate
the solvent-exposed
residues if that's needed. <br>
<br>
However, I think that no matter where you put the ions, they will
relocate once
the simulation equilibrates. So it may be better just to put enough
ions to
neutralise the system. You can then add some ions to reach the desired
ionic
strength. genion can be used to randomly put the ions in place, which
makes
sense since they're very mobile anyhow.<o:p></o:p></span></font></p>
</div>
<p class="MsoNormal"><font color="black" face="Times New Roman"
size="3"><span style="font-size: 12pt;"><br>
Hope that helps,<br>
Ran.<br>
<br>
Samuel C Flores wrote: <o:p></o:p></span></font></p>
<pre wrap=""><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;"> <o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;"><o:p> </o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">Hi Guys,<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;"><o:p> </o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;"> <o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;"><o:p> </o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">Can anyone tell me how I should go about adding counterions in GROMACS?<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">Right now I am adding just enough counterions to make the net charge equal<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">to zero. However I believe I should be adding a counterion for each charged<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">atom on the surface, according to some algorithm. Is there some program out<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">there, similar to Amber's CION, for deciding how many counterions to supply?<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">I think I can use genion to actually place them, right now I just want to<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">know how many I need..<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;"><o:p> </o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;"> <o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;"><o:p> </o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">Sam <o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;"><o:p> </o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;"><o:p> </o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;"> <o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;"> +++++++++++++++++++++++++++++++++++++++++++<o:p></o:p></span></font></pre>
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<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">_______________________________________________<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
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<br>
<br>
<o:p></o:p></span></font></p>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">-- <o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">------------------------------------------------------<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">Ran Friedman<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;"><a href="http://bioinfo.tau.ac.il/%7Eran">http://bioinfo.tau.ac.il/~ran</a><o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">Laser Laboratory for Fast Reactions in Biology<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
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<pre><font color="black" face="Courier New" size="2"><span
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<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">Tel. +972-3-6409824<o:p></o:p></span></font></pre>
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style="font-size: 10pt;">Fax. +972-3-6409875<o:p></o:p></span></font></pre>
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<br>
<pre class="moz-signature" cols="72">--
------------------------------------------------------
Ran Friedman
<a class="moz-txt-link-freetext" href="http://bioinfo.tau.ac.il/~ran">http://bioinfo.tau.ac.il/~ran</a>
Laser Laboratory for Fast Reactions in Biology
Department of Biochemistry
Faculty of Life Sciences
Tel-Aviv University
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Fax. +972-3-6409875
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