[gmx-users] Genion and number of Ions

David van der Spoel spoel at xray.bmc.uu.se
Wed Sep 25 17:06:19 CEST 2002

On Wed, 2002-09-25 at 15:01, Marc Saric wrote:
> Hi all,
> this might be a beginners question, but I have some problems with genion:
> I want to simulate a comparably large (~70 kDa) protein complex (three 
> single protein molecules one ligand and some water in a solvent-environment.
> I did all steps as described in the tutorial: pdb2gmx, addition of the 
> ligand-topology from PRODRG as described in the tutorial from John E. 
> Kerrigan, solvation with editconf and genbox, compilation with grompp, 
> addition of ions with genion.
> 1. Question: A friend of mine, who knows a bit more about MD-Simulation 
> than I, told me to make a neutral setup i.e. add as many ions as 
> necessary to bring the total charge to 0. Is there any other suggestion 
> (at the moment I add only a few Na+-Ions, but this doesn't sound  too 
> reasonable to me).
IIRC physiological salt concentration is 0.15 M. This means 1 ion per
183 waters. (55/0.15)x(Na + Cl- ). You can thus calculate roughly what
it should be. After neutralizing for your protein you add extra salt to
come to this concentration.

> 2. Question: What to do with fractional charges (i.e. -3.2 ?)
That is wrong. There must be an error in your topology.

> Is there any program or rule of thumb to decide on the amount of ions 
> necessary?
> 3. Question: Genion asks for a continuos solvent-group of single-atom 
> molecules. My solvent seems to be split in halfes, due to the 
> incorporation of the crystal-waters and later the addition of the ligand 
> and after that addition of the waterbox. Any hint how to overcome this 
> (beside processing the crystal-waters separately and adding them 
> afterwards by hand, which is quite tedious (renumbering etc.)).
Just use the solvent you added, for genion. Furthermore do use the
-random option for genion, the potential calculation is broken.

> Thanks in advance!
> -- 
> Bye,  Marc Saric
> Max-Planck-Institut fuer molekulare Physiologie
> Otto-Hahn-Str.11  44227 Dortmund  phone:0231/133-2168
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Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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