[gmx-users] Re: Counterions: influence on protein dynamics.
maxim.fedorov at ucd.ie
Wed Mar 1 00:26:36 CET 2006
> I'd guess that you're polylysine doesn't come charged without
> having any
> counterions in experiment.
Indeed, but if we are using classical non-polarisable FF
we already thrown off effects of protonation/deprotonation, charge
In the experiments, you're probably
> dealing with
> hydroxide ions (and an additional amount of hydronium ions). I'd
> say these
> will also influence the experimental findings. Therefore, there's
> more sense
> in adding counterions, maybe even positive and negative,
This is exactly the point - when I added MORE ions - the system
It leads to a bit higher salt concentration than it is in experiment,
after all this discussion I realized that it is better way than
constraining the ions.
> there is in
> creating a weird unphysical system.
> Have you also considered that not all of your lysines need to be
> protonatedat pH=7?
You'd actually want a constant-pH simulation
> with dynamic exchange
> of proteins. But that's one bridge too far at present :)
This is exactly what I want - but I guess I complete this project
before I will have a chance to use it :-)
> Good luck,
> On 2/28/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
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