Thanks, I did it manually using 'cat'. <br>Thanks for your time.<br><br>-Shivangi<br><br><div class="gmail_quote">On Mon, Mar 28, 2011 at 4:47 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br>
<br>
shivangi nangia wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi again,<br>
<br>
I did not quite understand the suggestion.<br>
I have successfully added Li+ ions in my simulation box using genion.<br>
I am confused about how to place Li+ ions using editconf.<br>
<br>
</blockquote>
<br></div>
Are these ions simply going to be part of the bulk solution? If so, use genion. Manual intervention is not necessary since random initial velocities will disrupt any sort of idealized geometry that you construct.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Will I have to create a .gro and .itp file and add it like a solute ?<br>
<br>
</blockquote>
<br></div>
Yes and no. If you really believe you need a specific location of a Li+ ion in your simulation cell, either (1) write a simple .gro file by hand and concatenate it with the coordinate file of your other system components or (2) use editconf -center to define its coordinates and concatenate that file with your system. Li+ parameters should be present in ions.itp for most force fields, so just #include that topology like you would any other system.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thanks,<br>
Shivangi<div class="im"><br>
<br>
<br>
<br>
On Mon, Mar 28, 2011 at 3:26 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
shivangi nangia wrote:<br>
<br>
Hello,<br>
<br>
I am a new gromacs user.<br>
<br>
I want to place Li+ ions at a required distance from the<br>
polypeptide ( which is at the centre of a box of water)<br>
<br>
I searched through the archive and the manual if there is a<br>
way/provision to do this, but could not.<br>
<br>
Is there a way?<br>
<br>
<br>
Measure the distance you want and establish the coordinate at which<br>
you wish to place the ion, then use editconf -center to place it at<br>
the proper location in the simulation box.<br>
<br>
-Justin<br>
<br>
<br>
<br>
Please guide.<br>
<br>
Thanks,<br>
Shivangi<br>
<br>
<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | <a href="tel:%28540%29%20231-9080" target="_blank">(540) 231-9080</a><br>
<tel:%28540%29%20231-9080><div class="im"><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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