[gmx-users] suspension of colloids in GROMACS

Justin Lemkul jalemkul at vt.edu
Thu Oct 22 18:41:09 CEST 2015

On 10/22/15 10:17 AM, CARDELLINI ANNALISA wrote:
> Dear gromacs users,
> In one project, I have to do some coarse grained molecular dynamics (CGMD)
> simulations of nano-colloids (inorganic particles 100-150 nm, 3%wt max very
> dilute) by using soft potentials (e.g. DLVO) and implicit solvent (Brownian
> dynamics or fluctuating hydrodynamics).
> 1) I am wondering if GROMACS is the right tool for that... I mean, in principle,
> it should be possible but is there explicit support for colloidal simulations?
> How can we introduced a proper force field for particles interactions?

You may want to look into the MARTINI models for biomolecular systems.  The 
approach would be the same.  There is no need for "explicit support" for what 
you're doing; GROMACS is an MD engine, like any other.  If supplied a valid 
physical model, you can simulate anything.  GROMACS even handles planets :)


> 2) Do you know someone in the GROMACS team doing colloidal simulations? Anyone
> else in the World?
> Your help would be highly appreciated.
> Best regards,
> Annalisa
> Annalisa Cardellini, M.Sc.
> Ph.D. student
> E-mail: annalisa.cardellini at polito.it
> SMaLL: http://www.polito.it/small


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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