Dear Mark,<br>thanks for your reply!<br><br>I'll try to better focus my issue: my intent is to perform simulations similar to which described in some
recently published papers in which cavities are expanded by means of LJ spheres, using methods
called "pressure guided MD" or "active-site pressurization" (Kimura et
al., Proteins 2008 Jan 3; Mazanetz et al., Biochemical Society
Transactions 2008). I'm working with a receptor model but experimental informations about
the ligand binding mode are not available to date. I don't want to
introduce bias in my MD simulations using a structure with the ligand
already inserted so, inspired by that papers, I was thinking about LJ spheres.<br><meta http-equiv="CONTENT-TYPE" content="text/html; charset=utf-8"><title></title><meta name="GENERATOR" content="OpenOffice.org 2.2 (Linux)"><meta name="AUTHOR" content="kia"><meta name="CREATED" content="20080219;16281800"><meta name="CHANGEDBY" content="kia"><meta name="CHANGED" content="20080219;16432900"><style type="text/css">
<!--
@page { size: 21cm 29.7cm; margin: 2cm }
P { margin-bottom: 0.21cm }
--></style>
How can I apply this approach with gromacs?<br><br>Chiara<br><br><br><br><div class="gmail_quote">On Feb 19, 2008 2:06 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> 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 class="Ih2E3d">Chiara Parravicini wrote:<br>> Hi Mark,<br>><br>> I just want make use of the volumes of the spheres to enlarge the pocket<br>
> without the use of any ligands.<br><br></div>How about using a ligand with charges set to zero? Or that and<br>tinkered-LJ parameters?<br><div><div></div><div class="Wj3C7c"><br>Mark<br>_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></div></div></blockquote></div><br>