On 14/12/10 19:04, Justin A. Lemkul wrote:
I was going to send a very similar mail -namely, I have a coarse-grain
system in vacuum where I'd like to simulate a charged polymer. My idea
was that of adding a single "ghost" counter-ion with zero VdW
interactions, perhaps keeping it fixed in one corner of the box, but
I'd like to know how meaningful it is.
"In vacuum" and "implicit solvent" are very different concepts. If you
are indeed simulating in a vacuum, I would be willing to bet that your
charged polymer will rapidly associate with your dummy ion simply due to
attractive Coulombic interactions that are not screened by any
intervening solvent.
Heh, I know very well that -and that is one of the reasons I wanted to
know how does one cope with that.
I mean, if it's a single polymer, perhaps one can naively position
restrain the ion in a corner of the box, away from the polymer, while
the polymer stays on its center of mass. But if I want multiple objects
in my box, I guess it's not going to work.
I'd like very much to use implicit solvent as well but I have to see how
deep is the performance impact on my model -after all, one does coarse
grain to be raw but *fast* :)
In regards to the original post, I have seen this question asked and
ignored several times already, unfortunately. Most of the literature I
have read (which primarily uses CHARMM) does not specify how counterions
are handled, if at all. Maybe there is some intrinsic compensating
factor in CHARMM that I simply don't know about. I found this:
http://dx.doi.org/10.1002/jcc.20874
But again, it uses CHARMM and fancy modified electrostatic models.
I would really hope that someone who knows about the proper GROMACS
methodology would comment. This has been a curiosity of mine for some
time, as well. I have not had a pressing need to try out the implicit
solvent features, but in the absence of being sure of the methodology, I
am unlikely to do so.
Perhaps the developers of the implicit solvent know about that? I hope so...
m.
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