[gmx-users] using implicit water for atomistic simulation of lipid bilayer

Justin Lemkul jalemkul at vt.edu
Sat Dec 10 20:48:46 CET 2016

On 12/9/16 5:58 PM, Mohsen Ramezanpour wrote:
> Dear Gromacs Users,
> I was wondering if there is any example of using Implicit water model for
> lipid bilayers in Gromacs?
> I have read on using implicit solvents in Gromacs and found interesting
> discussions:
> https://groups.google.com/forum/#!topic/archive-gmx-users/0HIFVop390I
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2011-December/066830.html
> As I understood, using implicit solvent assumes an infinite solvent around
> the solute.
> Which seems good for peptide/protein folding. I did not see any example for
> bilayers.
> Assuming that implicit solvent is well parameterized to work with lipid
> membranes, the one problem seems to be the PBC option in mdp file.
> PBC = no is appropriate for using implicit solvent while PBC = xyz is the
> usual case for bilayers.
> Is there any way to split the PBC treatment for water and bilayer? Like
> what we do in T-coupling for different groups.
> Also, I want to mix this implicit solvent with atomistic force field, like
> Gromos FF, not MARTINI.

I don't think GROMACS (or any other program) can handle this.  Perhaps you can 
get CHARMM to do it via the GBMW module, but even that (I'm pretty sure) 
requires an implicit bilayer (e.g. layers of high and low dielectric constant 
only, no mixture of explicit + implicit).



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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