<div>Hi Justin,</div>
<div>My aim is to add water inside the pore (I do not care about outside), so as you told me I used the first line of spc216.gro and I do not know why after the calculations that I posted before it says segmentation fault?? Thanks in advance/Jamie<br>
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<div class="gmail_quote">On Thu, Aug 13, 2009 at 2:41 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>Does it mean each time I can add one until I get the number that I want...?? Many Thanks/Jamie<br><br></div></blockquote><br>No need to do it manually. That's what -nmol is for.<br><font color="#888888"><br>
-Justin<br><br></font>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
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<div class="h5">On Thu, Aug 13, 2009 at 2:13 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><br> I made an insert.gro file for 2 water molecules, and when I<br> used genbox I got a fatal error: more than one residue in insert<br> molecules, program terminated.<br>
<br><br> Right, like I said before, the insert.gro file should contain<br> coordinates for *one* molecule.<br><br><br> I wanted to look at insert.gro, it does not show anything. And<br> when I convert it to pdb I got a warning [file aminoacids.dat,<br>
line 1]: Bad box file insert.gro<br><br><br> 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><br>
<br><br> When I looked at the insert.pdb file I found only 1.5 water<br> molecule! Which means 1 water plus a OH. Do you have any idea<br> what should I do or if I am missing some thing? Many Thanks in<br>
Advance/Jamie<br><br><br> I have no idea how you created this broken file, so I can't really<br> comment :) The easiest thing to do (I would think) would be to take<br> the first molecule of spc216.gro, keep the header lines, set number<br>
of atoms = 3 and preserve the box information at the bottom. I've<br> used that before in a few cases.<br><br> -Justin<br><br> On Thu, Aug 13, 2009 at 1:20 PM, 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>
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<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> 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>
<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>>><br> <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>><br>
<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<br> of the<br> pore<br> as well as a layer outside. From the "man genbox"<br>
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<br> 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<br> to 1.<br> 1. 1.,<br> the water molecules generated far away. I<br> appreciate if<br> someone<br>
tell me (1) how I can add water inside the pore<br> and (2) why<br><br><br> (1) The -vdwd option may help, or even -ci -nmol. If<br> you have a<br> pore, wouldn't water diffuse in over time anyway during<br>
equilibration (assuming an otherwise correct setup and<br> realistic<br> physical model)?<br><br> Long time ago I did an experiment on water in confined<br> geometry<br>
and I want to see if the results can obtain from the<br> simulation... So for using -nmol -ci (at random<br> position), it<br> says I must use a file like insert.gro would you please<br>
explain<br> me how I can make insert.gro?<br><br><br> The "insert.gro" file contains the coordinates of one<br> 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<br> the box, it<br> probably doesn't make any sense. The Gromacs<br> 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 -<br> 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.<br> Please<br> advise..Thanks in advance/Jamie<br><br><br> ------------------------------------------------------------------------<br>
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