[gmx-users] coordination file

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 18 20:06:44 CEST 2011

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.


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 

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.



> Cheers,
> Sarah K.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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