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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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