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On 1/04/2012 3:03 PM, Acoot Brett wrote:
<blockquote
cite="mid:1333256590.42780.YahooMailNeo@web121802.mail.ne1.yahoo.com"
type="cite">
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<div style="FONT-FAMILY: times new roman, new york, times,
serif; FONT-SIZE: 12pt">Dear All,</div>
<div style="FONT-FAMILY: times new roman, new york, times,
serif; FONT-SIZE: 12pt" class="ms__id616"> </div>
<div style="FONT-FAMILY: times new roman, new york, times,
serif; FONT-SIZE: 12pt" class="ms__id616">According to the
lysozyme model in the tutorial of <strong style="RIGHT:
auto">Justin Lemkul </strong>in <a
moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html</a>,
I am runing a 2 chain protein complex MD, and the steps are
exactly same as in that on-line tutorial except that I use
the 2 chain protein rather than laysozyme. In the
preparation steps, GROMACS produces 2 *.itp file,ne for
chain A, one for chain B. But in the following steps, I find
the 2 *.itp files have never been used by the following
command. Thus sometimes I am suspicious for the following
steps whether the MD was done only on Chain A or on both
Chains.</div>
<div style="FONT-FAMILY: times new roman, new york, times,
serif; FONT-SIZE: 12pt" class="ms__id616"> </div>
<div style="FONT-FAMILY: times new roman, new york, times,
serif; FONT-SIZE: 12pt" class="ms__id616">Will you please
clarify why GROMACS produces the 2 *.itp files but never
used them in the following MD steps? Have I done something
wrong on my 2 chain protein MD?<var id="yui-ie-cursor"></var></div>
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<br>
See manual 5.7.2 and <a
href="http://www.gromacs.org/Documentation/Include_File_Mechanism">http://www.gromacs.org/Documentation/Include_File_Mechanism</a><br>
<br>
Mark<br>
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