From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Oct 29 2008 - 17:39:03 CDT
On Wed, 29 Oct 2008, Christopher Gillespie wrote:
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
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?
CG> On Oct 29, 2008, at 5:56 PM, Emanuelle Bachelet wrote:
CG> >Hi Chris,
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> >I will also have a look at the reference you mention.
CG> >On Wed, Oct 29, 2008 at 4:05 PM, Christopher Gillespie
CG> ><gillescche_at_gmail.com> wrote:
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> >On Oct 29, 2008, at 2:44 PM, Emanuelle Bachelet wrote:
CG> >I have a question regarding ions in a simulation.
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> >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?
-- ======================================================================= 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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