<div>Hi Justin,</div>
<div>Thanks for your answer,<br></div>
<div class="gmail_quote">On Thu, Aug 13, 2009 at 11:42 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im"><br><br>Jamie Seyed wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Dear all,<br>I want to know how can I use genbox to fill inside of the pore as well as a layer outside. From the "man genbox" page I try to use -shell with a negative value (?) but it put waters far from the outside of the pore and I think it does not care about the sign. It seems strange to me because when I had 10 10 10 in the last line of my f.gro, by a shell 0.5 or 0.2, I got a layer of few molecule around the pore, but when I change it to 1. 1. 1., the water molecules generated far away. I appreciate if someone tell me (1) how I can add water inside the pore and (2) why <br>
</blockquote><br></div>(1) The -vdwd option may help, or even -ci -nmol. If you have a pore, wouldn't water diffuse in over time anyway during equilibration (assuming an otherwise correct setup and realistic physical model)?</blockquote>
<div> </div>
<div>Long time ago I did an experiment on water in confined geometry and I want to see if the results can obtain from the simulation... So for using -nmol -ci (at random position), it says I must use a file like insert.gro would you please explain me how I can make insert.gro? </div>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><span id=""></span><br>(2) If you haven't re-positioned your system within the box, it probably doesn't make any sense. The Gromacs convention is to place the corner of the box at the coordinate origin, and everything else is relative to that. Is a 1-nm cubic box large enough to encompass your system? If not, genbox is doing what it's told - filling a 1-nm box near the origin, and leaving everything else out.</blockquote>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><span id=""></span><br><br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im">changing the box size will give a opposite result. Please advise..Thanks in advance/Jamie<br><br><br></div>------------------------------------------------------------------------<br><br>_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.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 www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">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></blockquote><br>-- <br>========================================<br><br>Justin A. Lemkul<br>
Ph.D. Candidate<br>ICTAS Doctoral Scholar<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>
<br>========================================<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.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 www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">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></blockquote></div><br>