Hi Per (and all),
I am trying to recreate the results of the CHARMM forcefield
implementation to better understand how to implement implicit solvent
models, but I can't quite recreate your results. If the Gromacs code
doesn't use salt concentrations, does that mean that your simulations
were run at zero salt concentration? Also, how did you deal with the
charged residues on the protein?
Also, sort of on the same topic, no matter what option I choose for
sa_algorithm with Gromacs 4.5.3, it always uses sa_algorithm=Still.
Thanks for your help,
Rogan
On Dec 14, 2010, at 12:13 PM, Per Larsson wrote:
Hi!
Sorry that I missed this discussion, we recently moved the lab and
there where quite many things to attend to.
When we did the implementation of implicit solvent into Gromacs, one
of the strong points was to see how fast we could make it, to speed
up conformational sampling as much as possible. Adding in the extra
Debye-Huckel term for a non-zero salt-concentration was not a
priority at the time. It might be a bit unfortunate that the option
anyway exists in the mdp-file.
I will try and see if I can find the time to put it in, but that
will not happen in the next coming weeks although I agree that it
would be very useful to have :-)
When it comes to the use of explicit ions in an implicit solvent, I
hate to say that I'm not much of an expert, really. Having said
that, and someone else is very welcome to correct me on this point,
there does not seem to exist a wide body of literature about this.
In addition to the paper that Justin pointed to, there is some work
done by Michael Feig (eg. http://www.ncbi.nlm.nih.gov/pubmed/
16928023).
Also I think that particularly with DNA there are problems with the
theory itself as it does not handle high salt-concentrations very
well.
Cheers
/Per
14 dec 2010 kl. 20.22 skrev devicerandom:
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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