<div>Hi Justin,</div>
<div>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.</div>
<div>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</div>
<div>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></div>
<div class="gmail_quote">On Thu, Aug 13, 2009 at 1:20 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">
<div class="im">Hi Justin,<br>Thanks for your answer,<br></div>
<div class="im">On Thu, Aug 13, 2009 at 11:42 AM, 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> Dear all,<br> I want to know how can I use genbox to fill inside of the pore<br> as well as a layer outside. From the "man genbox" page I try to<br> use -shell with a negative value (?) but it put waters far from<br>
the outside of the pore and I think it does not care about the<br> sign. It seems strange to me because when I had 10 10 10 in the<br> last line of my f.gro, by a shell 0.5 or 0.2, I got a layer of<br> few molecule around the pore, but when I change it to 1. 1. 1.,<br>
the water molecules generated far away. I appreciate if 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 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? <br>
<br></div></blockquote><br>The "insert.gro" file contains the coordinates of one molecule that you want to insert, i.e. one water molecule.<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"> (2) If you haven't re-positioned your system within the box, it<br> probably doesn't make any sense. The Gromacs convention is to place<br> the corner of the box at the coordinate origin, and everything else<br>
is relative to that. Is a 1-nm cubic box large enough to 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>
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<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>
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