[gmx-users] Ions close to protein

David van der Spoel spoel at xray.bmc.uu.se
Tue May 23 20:13:32 CEST 2006

David Mobley wrote:
> Joanne,
>> >When I add ions to my system to neutralise it some are placed quite 
>> close to the protein (even when using random) and in other cases 
>> during simualtions I have seen ions move into the protein, is this 
>> normal/okay and are there any ways of keeping these ions away from the 
>> protein?
> In terms of keeping them away from the protein, not too sure. But I
> think it is right to be nervous about ions that move into your
> protein. These could have long correlation times.  Depending on how
> long the correlation times are, you might need to run longer to get
> adequate sampling. On the other hand, if your salt concentration is
> reasonable, you might have enough ions that this behavior will
> appropriately average out, especially if correlation times are
> relatively short.
> Probably, the overall answer to whether this is okay depends on what
> question you are trying to ask. My personal opinion is that ions are a
> whole can of worms that is mostly unopened so far, but sooner or later
> someone will have to open it and it will be messy (long correlation
> times, bad parameters, and strongly influence certain things). But
> perhaps I'm just being pessimistic. And, in fairness, I should say
> that so far I've decided just to ignore the issue, because I don't
> want to be the guy who opens the can of worms.

OK, better show a glimpse of what's in the can then...

We are finishing a paper about this stuff, and the conclusion is: no 
problem as long as your simulations are reasonably long and you use PME. 
Charged sidechains have *on average* half a counterion in our tests. A 
real problem may be that force fields are not adapted to having 
realistic ionic strength, and hence you might influence protein 
stability by introducing. This is very hard to prove however.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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