[gmx-users] Polarizable Li+ Drude Simulations

Justin Lemkul jalemkul at vt.edu
Tue Nov 17 18:31:33 CET 2015

On 11/17/15 12:18 PM, Tuanan Lourenço wrote:
> Hi, My name is Tuanan and I am a Ph.D Student from Brazil.
> I am trying simulate Li+ using the polarizable force field of Roux (J.
> Chem. Theor. Comput., (2010), 6, 774-786) but I don't understand how i
> create my Li+ structure PDB file.
>   I must insert a Drude particle in Li+ PDB file??? Someone would have a
> tutorial or a example of PDB file of monovalent ion with polarizable force
> field based on Drude?

The initial coordinates of the Drude particle are the same as the parent atom. 
Following minimization and/or propagation in dynamics, the Drude moves in 
response to the surrounding environment.

Have a look at http://mackerell.umaryland.edu/charmm_drude_ff.shtml if you want 
the latest features for simulating polarizable systems.  It's not in an official 
release (it's on my still-too-long to-do list) but the instructions are there, 
as well as sample .mdp files.  The code has a modified genion that inserts 
polarizable ions for you, though this is really a trivial operation, as noted above.



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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