Re: ions behavior in protein-water box:

From: Christopher Gillespie (gillescche_at_gmail.com)
Date: Thu Oct 30 2008 - 13:50:38 CDT

Ema,

Given enough simulation time, and as Axel already mentioned the longer
range coulombic effects, I would expect either Ca or Na to associate
with Asp or Glu residues. The only other option is no ions, but PME
really should have a neutral system.

Chris

On Oct 30, 2008, at 1:24 PM, Emanuelle Bachelet wrote:

> Actually, one the Ca ions comes close to an aspartic acid - this is
> so not good!
>
> Well, one simulation I am trying now is to just fix the ions around
> their equilibrated positions - (all these are more than 10A from any
> protein atom after I finished equilibration). I will monitor the
> progress and if it dosen't work I will introduce 9 sodium ions - I
> hope I won't have to make the water box bigger to accomodate all of
> them.
>
> I used Ca ions so I could keep the water box reasonable size and
> keep ions at large distance from each other (instead of having 9
> sodium ions since I deleted the waters manually and put the ions in
> place of those 5 water molecules). But i didn't think earlier that
> the Ca2+ will have such dramatic effects.
>
> Many thanks,
> Ema.
>
>
> On Wed, Oct 29, 2008 at 6:39 PM, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu
> > wrote:
> On Wed, 29 Oct 2008, Christopher Gillespie wrote:
>
> CG> Ema,
> CG>
> CG> I agree that the ions shouldn't effect the protein dramatically,
> but if you
> CG> are concerned with the interactions of the ions with the protein
> why include
> CG> the Ca2+ and not just Na+? If the protein is not restrained in
> any way the
> CG> ion effect over the length of the simulation should not be too
> dramatic.
> CG> Simple Brownian motion is going to move the ions with or without
> the
> CG> protein.
>
> to add to this: if you put a -9 charged object somewhere,
> it _is_ highly attactive to objects of the opposite charge,
> and doubly so for calciums. ;-)
>
> coulomb interactions are quite strong and range far, so
> i would not be too surprised to have some cations sticking
> rather closely to your protein. do you know for sure that
> there are none? how deeply are the anionic components buried?
>
> cheers,
> axel.
>
>
> CG>
> CG> Best,
> CG> Chris
> CG>
> CG>
> CG> On Oct 29, 2008, at 5:56 PM, Emanuelle Bachelet wrote:
> CG>
> CG> >Hi Chris,
> CG> >
> CG> >By closer I mean less than 5A, I haven't measured the exact
> distance
> CG> >because it's fluctuating. But imo, less than 5A means ions are
> going to
> CG> >modify the electrostatic interactions with/on the protein. Ions
> should be
> CG> >just to neutralize the system not to interact with the protein.
> CG> >
> CG> >I will also have a look at the reference you mention.
> CG> >
> CG> >Thanks,
> CG> >Ema
> CG> >
> CG> >On Wed, Oct 29, 2008 at 4:05 PM, Christopher Gillespie
> CG> ><gillescche_at_gmail.com> wrote:
> CG> >Ema,
> CG> >
> CG> >What exactly do you mean by "closer"? Ion association with
> protein
> CG> >surfaces is not necessarily an "incorrect" observation rather
> ions can
> CG> >interact with various parts routinely. Take a look at the work
> of Pavel
> CG> >Jungwirth on ion protein association.
> CG> >
> CG> >Best
> CG> >
> CG> >Chris
> CG> >
> CG> >
> CG> >
> CG> >On Oct 29, 2008, at 2:44 PM, Emanuelle Bachelet wrote:
> CG> >
> CG> >Hello,
> CG> >
> CG> >I have a question regarding ions in a simulation.
> CG> >
> CG> >I have a protein that has a net charge of -9 (it includes one
> of the
> CG> >residues which is phosphorylated). I immersed this protein in
> water box it
> CG> >and added 4 calcium ions and one sodium ion to neutralize the
> overall
> CG> >charge.
> CG> >
> CG> >But when my simulation system reaches .5ns of production
> dynamics (NVE),
> CG> >some ions move closer to the protein. In my opinion, they
> should not come
> CG> >too close to protein so as to modify the protein behavior. Does
> this mean
> CG> >that I constrain the ions at a particular position?
> CG> >
> CG> >thanks,
> CG> >Ema.
> CG> >
> CG> >
> CG>
> CG>
>
> --
> =
> ======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://
> www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA
> 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =
> ======================================================================
> If you make something idiot-proof, the universe creates a better
> idiot.
>

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