[gmx-users] Implicit "solvation" at air-water interface

Justin Lemkul jalemkul at vt.edu
Sat Jan 11 02:35:24 CET 2014

On 1/10/14, 12:37 PM, Michael Daily wrote:
> Hi all,
> I have been conducting simulations of peptoids (a cousin of peptides) in
> implicit solvent in gromacs, which in conjunction with REMD has been very
> useful for sampling the conformational distribution.
> Since some of the peptoids are amphiphilic, I'm also interested in
> simulating them implicitly at an air/water or (nonpolar solvent)/water
> interface.  That is, I'd like to have a box split into high- and
> low-dielectric regions.  Does this functionality exist in gromacs or is it
> planning to be developed?

No, and probably not.  A distance-dependent dielectric may have been mentioned 
once or twice across the list, but I don't know that anyone's working on it. 
Feature requests can be filed on Redmine, but unless a core developer has a 
strong desire to do it, it's up to the community to contribute it.



Justin A. Lemkul, Ph.D.
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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