[gmx-users] coordination file

Mark Abraham 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
>> 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 

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. 


> -Justin
>> Cheers,
>> Sarah K.

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