[gmx-users] Re: Counterions: influence on protein dynamics.

Maxim Fedorov maxim.fedorov at ucd.ie
Wed Mar 1 00:26:36 CET 2006

Dear Tsjerk
> Maxim,
> 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 
transfer etc,
do we?
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 
behaves better.
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 :-)
Many thanks,
> Good luck,
> Tsjerk
> On 2/28/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> >

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