Hi <br><br>I want to use a solvent with two types molecules (for example linear and cyclic Glucose form).<br>How can I fill box with them?<br><br>I highly appreciate for advice given me!<br><br>Best Regards<br>Rasoul<br><br>
<div class="gmail_quote">On Sat, Jan 16, 2010 at 11:42 AM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</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;">
<div><div></div><div class="h5">leila karami 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 David<br>
in genbox command system solvated by water molecule by default. but I want solvent except water.<br>
leila karami<br>
<br>
</blockquote></div></div>
OK, now I understand.<br>
<br>
You can give to genbox any solvent that you like, provided that each molecule consists of a single residue (the residue number is used to distinguish molecules). In the gromacs distribution there are a couple of other solvents present. Look in share/gromacs/top directory of your installation (or roll your own).<br>
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>
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