On 4/19/2011 4:06 AM, Justin A. Lemkul wrote:
sarah k wrote:
Dear gromacs users,
Thanks for your previous guidance. I used Drug/Enzyme complex
solvation tutorial to run my simulation in nitrogen box. It finally
worked.
But I think that the *.gro coordination file of my solvent has problem
beacuse when I run it, in my _b4ion.gro file the nitrogen molecules
have overlapped and created connected triangles near the protein where
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.
they are more dense. Since nitrogen is gas, I can not make a dense
box. If the nitrogen molecules in my gro file be more than 60, the
protein structure breaks and energy minimization can't take place. If
it be few I'll confront this error when I type mdrun_d -s a_pr.tpr -o
a_pr.trr -c a_b4md.gro -g pr.log -e pr.edr &:
2 particles communicated to PME node 1 are more than a cell length of
their charge group.
(I've optimized the #solvent molecules and I guess 49 is the best.)
If I define a larger box of 2.1 the error changes to:
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.
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated.
Both of your errors indicate that your system is blowing up.
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
Your system has become unstable either due to a poor topology, bad
starting configuration, incorrect .mdp settings, or a combination of
these.
Thus, I think that all the problem is the coordination file of
nitrogen. I need a nitrogen box with its coordinations and
pre-equilibrating it. Is it really my problem? Can someone explain how
I can generate a pre-equilibrated coordination file similar to
spc216.gro but with nitrogen? Thanks.
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:
1. Search the literature for previous similar attempts and try to
replicate that methodology.
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.
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.
http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation
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
http://lists.gromacs.org/pipermail/gmx-users/2011-April/060408.html
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.
<http://lists.gromacs.org/pipermail/gmx-users/2011-April/060408.html>
Mark
-Justin
Cheers,
Sarah K.
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