[gmx-users] coordination file
Mark.Abraham at anu.edu.au
Tue Apr 19 02:30:47 CEST 2011
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
>> 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.
> Your system has become unstable either due to a poor topology, bad
> starting configuration, incorrect .mdp settings, or a combination of
>> 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,
> 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.
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
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.
>> Sarah K.
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