Re: ions behavior in protein-water box:

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Thu Oct 30 2008 - 13:40:45 CDT

Ema,

It is still not clear why you are concerned about the ions approaching
your protein. The ions are just behaving according to the physics
dictated by whatever force field you are using. In fact it is
unphysical to sequester the ions away from the protein. If you do this
with an external force you are restraining your simulation out of
equilibrium. The only time you should be concerned is if an ion
becomes buried inside the protein due to some anomalous fluctuation or
poor initialization.

Simply put, unless you have a good physical reason to do so, you
should not be restraining the position of your ions.

Josh

On Oct 30, 2008, at 10:24 AM, 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.
>

------------------------------------------------------------------------------------------------------
Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/~jadelman
Berkeley, CA 94720 USA jadelman_at_berkeley.edu
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