<div>Hi Justin,</div>
<div>Does it mean each time I can add one until I get the number that I want...?? Many Thanks/Jamie<br><br></div>
<div class="gmail_quote">On Thu, Aug 13, 2009 at 2:13 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="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><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">Hi Justin,
<div class="im"><br>I made an insert.gro file for 2 water molecules, and when I used genbox I got a fatal error: more than one residue in insert molecules, program terminated.<br></div></blockquote><br>Right, like I said before, the insert.gro file should contain coordinates for *one* molecule.
<div class="im"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">I wanted to look at insert.gro, it does not show anything. And when I convert it to pdb I got a warning [file aminoacids.dat, line 1]: Bad box file insert.gro<br>
</blockquote><br></div>Well, how did you make this file? A .gro file has a specific format:<br><br><a href="http://manual.gromacs.org/current/online/gro.html" target="_blank">http://manual.gromacs.org/current/online/gro.html</a>
<div class="im"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">When I looked at the insert.pdb file I found only 1.5 water molecule! Which means 1 water plus a OH. Do you have any idea what should I do or if I am missing some thing? Many Thanks in Advance/Jamie<br>
<br></blockquote><br></div>I have no idea how you created this broken file, so I can't really comment :) The easiest thing to do (I would think) would be to take the first molecule of spc216.gro, keep the header lines, set number of atoms = 3 and preserve the box information at the bottom. I've used that before in a few cases.<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">On Thu, Aug 13, 2009 at 1:20 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> Jamie Seyed wrote:<br><br> Hi Justin,<br> Thanks for your answer,<br> On Thu, Aug 13, 2009 at 11:42 AM, Justin A. Lemkul<br> <<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>><br>
</div>
<div>
<div></div>
<div class="h5"> <mailto:<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> Jamie Seyed wrote:<br>
<br> Dear all,<br> I want to know how can I use genbox to fill inside of the<br> pore<br> as well as a layer outside. From the "man genbox" page I<br> try to<br>
use -shell with a negative value (?) but it put waters<br> far from<br> the outside of the pore and I think it does not care<br> about the<br> sign. It seems strange to me because when I had 10 10 10<br>
in the<br> last line of my f.gro, by a shell 0.5 or 0.2, I got a<br> layer of<br> few molecule around the pore, but when I change it to 1.<br> 1. 1.,<br> the water molecules generated far away. I appreciate if<br>
someone<br> tell me (1) how I can add water inside the pore and (2) why<br><br><br> (1) The -vdwd option may help, or even -ci -nmol. If you have a<br> pore, wouldn't water diffuse in over time anyway during<br>
equilibration (assuming an otherwise correct setup and realistic<br> physical model)?<br><br> Long time ago I did an experiment on water in confined geometry<br> and I want to see if the results can obtain from the<br>
simulation... So for using -nmol -ci (at random position), it<br> says I must use a file like insert.gro would you please explain<br> me how I can make insert.gro?<br><br><br> The "insert.gro" file contains the coordinates of one molecule that<br>
you want to insert, i.e. one water molecule.<br><br> -Justin<br><br> (2) If you haven't re-positioned your system within the box, it<br> probably doesn't make any sense. The Gromacs convention is<br>
to place<br> the corner of the box at the coordinate origin, and<br> everything else<br> is relative to that. Is a 1-nm cubic box large enough to<br> encompass<br> your system? If not, genbox is doing what it's told - filling a<br>
1-nm box near the origin, and leaving everything else out.<br><br><br><br> -Justin<br><br> changing the box size will give a opposite result. Please<br> advise..Thanks in advance/Jamie<br>
<br><br> ------------------------------------------------------------------------<br><br> _______________________________________________<br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>><br>
<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><br>
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" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>><br> <mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>>.<br><br> Can't post? Read<br> <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<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></div></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="http://vt.edu/" target="_blank">http://vt.edu/</a>> | (540)
<div class="im"><br> 231-9080<br><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> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
</div> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>>
<div>
<div></div>
<div class="h5"><br><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<br>
posting!<br> Please don't post (un)subscribe requests to the list. Use the www<br> interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>><br> <mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>>.<br><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>
<br><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> <<a href="http://vt.edu/" target="_blank">http://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> <mailto:<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<br> posting!<br> Please don't post (un)subscribe requests to the list. Use the www<br>
interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br> <mailto:<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><br><br></div></div></blockquote>
<div>
<div></div>
<div class="h5"><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></div></div></blockquote></div><br>