[gmx-users] semi-permeable wall in gromacs

Justin Lemkul jalemkul at vt.edu
Wed Mar 9 18:30:56 CET 2016

On 3/9/16 12:28 PM, gozde ergin wrote:
> Dear all,
> I would like to compute the osmotic pressure directly from all-atom MD simulations of concentrated aqueous solutions.
> The basic idea is to introduce “virtual” walls to represent the effect of ideal semipermeable membranes, separating a high concentration region from a pure water region.
> The walls keep the ions confined, but the water molecules are allowed to pass freely, permitting an equalization of their chemical potential throughout the entire system.
> The mean force per unit area exerted on the ions by the virtual walls during the simulations can be directly related to the osmotic pressure.
> My question is is there a way to introduce semi-permeable walls in GROMACS?

Use flat-bottom restraints on the ions.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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