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On 26/10/2011 5:18 PM, cuong nguyen wrote:
<blockquote
cite="mid:CAMj9Mafee66DBim=54X3EWN3YaJ_aAgeNCiFN+H2qWwBPgKWDQ@mail.gmail.com"
type="cite">Dear Mark,<br>
<br>
I used to put ten molecules of hexanol in a box 5 5 1 with the
instruction "genbox -ci hexanol.gro -nmol 10 -box 5 5 1 -o
layer.gro -p hexanol.top". However, now I want to fill up the box
4 4 4 with hexanol molecules.<br>
If I change the number 10 in the instruction to 1000 or 10000, it
will run well but I do not know if this box is full.<br>
Please help me to change this instruction.<br>
</blockquote>
<br>
It probably can't be full. genbox -ci does not generate a close
packing, so the first part of your procedure isn't useful, as you
would have learned from reading genbox -h. See <a
href="http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation">http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation</a>
for a sound workflow.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAMj9Mafee66DBim=54X3EWN3YaJ_aAgeNCiFN+H2qWwBPgKWDQ@mail.gmail.com"
type="cite"><br>
Thanks a lot.<br>
<br>
Regards,<br>
<br>
Cuong<br>
<br>
<div class="gmail_quote">2011/10/26 Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im">On 26/10/2011 1:46 PM, cuong nguyen wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear,<br>
<br>
Thanks a lot for useful software. I am trying to generate
a box (4 4 4) with full hexanol molecules inside. I have
used the instruction "genbox -ci hexanol.GRO -box 4 4 4 -o
layer.gro -p hexanol.top", however it has not been
successful.<br>
</blockquote>
<br>
</div>
Unfortunately we can't help if we don't know what is in your
-ci box (also, it's probably best not to use capitalized
filename extensions), or why you think the procedure was not
successful. Please consider the advice here <a
moz-do-not-send="true" href="http://www.gromacs.org/Support"
target="_blank">http://www.gromacs.org/Support</a>.<br>
<br>
Mark<br>
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</font></blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
<div>Nguyen Van Cuong</div>
<div>PhD student - Curtin University of Technology</div>
<div>Mobile: (+61) 452213981</div>
<div> </div>
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