<font style="font-family: arial narrow,sans-serif;" size="4">Hi,<br>Thanks for the replies.<br>Since I want to increase distance among co-solvents with themselves and with solutes, i must firstly fill the co-solvents along solutes and solvents after that i remove solvent, finally by edittconf -translate the co-solvents uniformally is distributed in the appropriate distances. Is it OK?<br>
<br>Rasoul<br></font><br><div class="gmail_quote">On Sat, Apr 17, 2010 at 5:43 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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<br>
Justin A. Lemkul wrote:<div class="im"><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<br>
rasoul nasiri wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Justin,<br>
Hello again<br>
<br>
Thanks for the message. I want to increase the distance between solutes in simulation box before MD simulation. How can I do it?<br>
<br>
</blockquote>
<br>
You can't. If you know you need a certain distance, that should be part of your planning :) I suppose you could run a pulling simulation to separate your two species, but that requires substantially more work (and setup considerations) than the two or three quick editconf commands to properly build the system.<br>
<br>
</blockquote>
<br></div>
Correction: you can use editconf -translate with appropriate index groups to separate your solutes. This will also imply that you haven't added solvent, which is the same thing as positioning the two solutes appropriately in the first place (with editconf -center, as I posted before).<br>
<font color="#888888">
<br>
-Justin</font><div><div></div><div class="h5"><br>
<br>
-- <br>
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<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> | (540) 231-9080<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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