[gmx-users] Neutralize or add an Ions Concentration for a Membrane Simulation?

Justin Lemkul jalemkul at vt.edu
Sat Mar 8 14:36:03 CET 2014

On 3/7/14, 11:14 PM, Andres Ortega wrote:
> Hi Dear Gromacs Users, i would like to ask you something,
> My system consist of an ion channel , and a drug molecule, i´m preparing a
> umbrella simulation,
> to study the PME between the protein and the molecule, so , i´ve been
> reading papers, and some of them
> just add ions to neutralize the system, but other just use a concentration
> of KCL ,
> What do you think is the best option for me(considering my system), and how
> is the effect to add a concentration of ions, is it cause more computation ?

Ions don't add significant computational effort.  In fact, genion replace water 
molecules with ions, so it really reduces the number of atoms in the system.

The real answer is that it depends.  Ion type and concentration depend on what 
is relevant to your system and its physiological conditions.  If it is the ion 
channel is specific to a particular type of ion and you're interested in 
transport properties, then the choice is rather clear.  Concentration depends on 
what experimental conditions you are trying to study.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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