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Hi,<br>
<br>
<div align="justify">
<div align="justify">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.<br>
</div>
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.<br>
</div>
<br>
Hope that helps,<br>
Ran.<br>
<br>
Samuel C Flores wrote:
<blockquote
cite="mid200607161633.k6GGX3dm024214@pantheon-po11.its.yale.edu"
type="cite">
<pre wrap="">
Hi Guys,
Can anyone tell me how I should go about adding counterions in GROMACS?
Right now I am adding just enough counterions to make the net charge equal
to zero. However I believe I should be adding a counterion for each charged
atom on the surface, according to some algorithm. Is there some program out
there, similar to Amber's CION, for deciding how many counterions to supply?
I think I can use genion to actually place them, right now I just want to
know how many I need..
Sam
+++++++++++++++++++++++++++++++++++++++++++
This Mail Was Scanned By Mail-seCure System
at the Tel-Aviv University CC.</pre>
<pre wrap="">
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<br>
<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
Tel. +972-3-6409824
Fax. +972-3-6409875
------------------------------------------------------
</pre>
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