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On 22/04/2012 1:13 AM, Shima Arasteh wrote:
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cite="mid:1335021230.43506.YahooMailNeo@web36408.mail.mud.yahoo.com"
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<div><span>So I can not change the type of unit cell in
regenerating a job done before, right?</span></div>
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<br>
You can't replicate the simulation (see, for example,
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/Terminology/Reproducibility">http://www.gromacs.org/Documentation/Terminology/Reproducibility</a>).
You can attempt to replicate the observations. If you judge they're
independent of box shape, then use whatever box you want.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:1335021230.43506.YahooMailNeo@web36408.mail.mud.yahoo.com"
type="cite">
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<div><br>
<span></span></div>
<div><span>Cheers, <br>
</span></div>
<div><span>Shima<br>
</span></div>
<div><br>
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<div style="font-family: times new roman, new york, times,
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<div dir="ltr"> <font face="Arial" size="2">
<hr size="1"> <b><span style="font-weight:bold;">From:</span></b>
Mark Abraham <a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a><br>
<b><span style="font-weight: bold;">To:</span></b>
Discussion list for GROMACS users
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a> <br>
<b><span style="font-weight: bold;">Sent:</span></b>
Saturday, April 21, 2012 7:23 PM<br>
<b><span style="font-weight: bold;">Subject:</span></b>
Re: [gmx-users] Type of unit cell<br>
</font> </div>
<br>
<div id="yiv1157240376">
<div> On 22/04/2012 12:00 AM, Shima Arasteh wrote:
<blockquote type="cite">
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0);background-color:rgb(255, 255,
255);font-family:arial, helvetica,
sans-serif;font-size:12pt;">
<div>Dear Gomacs friends,</div>
<div><br>
</div>
<div>I'd like to know if it makes different in the
last outcomes of a simulation when I change the
box? </div>
</div>
</blockquote>
<br>
Yes, it changes.<br>
<br>
<blockquote type="cite">
<div style="color:rgb(0, 0,
0);background-color:rgb(255, 255,
255);font-family:arial, helvetica,
sans-serif;font-size:12pt;">
<div>For example I use <font face="Arial"><font
size="3">dodecahedron instead of cubic one. I
just know that I need to add less numbers of
water molecules.</font></font></div>
</div>
</blockquote>
<br>
True. It's your call based on what you want to simulate.<br>
<br>
Mark<br>
</div>
</div>
<br>
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