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On 4/19/2011 4:06 AM, Justin A. Lemkul wrote:
<blockquote cite="mid:4DAC7DB4.5070604@vt.edu" type="cite">
<br>
<br>
sarah k wrote:
<br>
<blockquote type="cite">Dear gromacs users,
<br>
<br>
Thanks for your previous guidance. I used Drug/Enzyme complex
<br>
solvation tutorial to run my simulation in nitrogen box. It
finally
<br>
worked.
<br>
<br>
But I think that the *.gro coordination file of my solvent has
problem
<br>
beacuse when I run it, in my _b4ion.gro file the nitrogen
molecules
<br>
have overlapped and created connected triangles near the protein
where
<br>
</blockquote>
<br>
To be clear, there are no such connections. Your visualization
software is simply using a heuristic algorithm to guess where
bonds should be based on interatomic distances.
<br>
<br>
<blockquote type="cite">they are more dense. Since nitrogen is
gas, I can not make a dense
<br>
box. If the nitrogen molecules in my gro file be more than 60,
the
<br>
protein structure breaks and energy minimization can't take
place. If
<br>
it be few I'll confront this error when I type mdrun_d -s
a_pr.tpr -o
<br>
a_pr.trr -c a_b4md.gro -g pr.log -e pr.edr &:
<br>
2 particles communicated to PME node 1 are more than a cell
length of
<br>
their charge group.
<br>
<br>
(I've optimized the #solvent molecules and I guess 49 is the
best.)
<br>
<br>
If I define a larger box of 2.1 the error changes to:
<br>
</blockquote>
<br>
A 2.1-nm box? For all but the smallest proteins (or even a single
amino acid, for that matter) and shortest cutoffs, this is
certainly far too small.
<br>
<br>
<blockquote type="cite">A charge group moved too far between two
domain decomposition steps
<br>
This usually means that your system is not well equilibrated.
<br>
<br>
</blockquote>
<br>
Both of your errors indicate that your system is blowing up.
<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up">http://www.gromacs.org/Documentation/Terminology/Blowing_Up</a>
<br>
<br>
Your system has become unstable either due to a poor topology, bad
starting configuration, incorrect .mdp settings, or a combination
of these.
<br>
<br>
<blockquote type="cite">Thus, I think that all the problem is the
coordination file of
<br>
nitrogen. I need a nitrogen box with its coordinations and
<br>
pre-equilibrating it. Is it really my problem? Can someone
explain how
<br>
I can generate a pre-equilibrated coordination file similar to
<br>
spc216.gro but with nitrogen? Thanks.
<br>
</blockquote>
<br>
It is important to not draw simple analogies like "how can I make
nitrogen like water." You can immediately see that there is a
problem with that logic. If you want to simulate a protein in the
gas phase, you should:
<br>
<br>
1. Search the literature for previous similar attempts and try to
replicate that methodology.
<br>
<br>
2. Be sure that you're using gas phase conditions (usually NVT
instead of NPT to avoid spurious contraction of the box),
appropriate cutoffs, etc.
<br>
<br>
You can equilibrate any sort of "solvent" you wish, liquid or gas,
by applying the correct conditions, although all of the force
fields implemented in Gromacs have principally been validated for
condensed phase simulations. That said, it doesn't mean you can't
accomplish your goal, but your workflow and .mdp settings may have
to be somewhat different from the standard tutorials of proteins
in water.
<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation">http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation</a>
<br>
</blockquote>
<br>
And to generate such a solvent box, one good procedure can be found
by following the links I've posted twice before in response to
Sarah's posts. See <a
href="http://lists.gromacs.org/pipermail/gmx-users/2011-April/060408.html">http://lists.gromacs.org/pipermail/gmx-users/2011-April/060408.html</a><br>
<br>
I'm now going to stop helping on this topic. I have better things to
do than have my solutions ignored while people keep posting problems
encountered with their attempted solutions. <a
href="http://lists.gromacs.org/pipermail/gmx-users/2011-April/060408.html"></a><br>
<br>
Mark<br>
<br>
<blockquote cite="mid:4DAC7DB4.5070604@vt.edu" type="cite">
<br>
-Justin
<br>
<br>
<blockquote type="cite">
<br>
Cheers,
<br>
Sarah K.
<br>
</blockquote>
<br>
</blockquote>
<br>
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