[gmx-users] coordination file

[Mark Abraham]

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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