[gmx-users] Regarding creating a box around the molecule and neutralization of charge before EM and MD

[Justin Lemkul]

On 7/21/17 9:58 AM, S M Bargeen Turzo wrote:
> In order to do an energy minimization and md simulation is it a must to
> create a box around your molecule of interest(whether it be a small or
> macro molecule). If so can you please explain why?
> 

Depends on what you want to model.  If you want to simulate in the condensed 
phase, generally a box full of water is necessary.  Neutralizing ions aren't 
strictly necessary with PME due to the neutralizing background plasma, but is 
required in many heterogeneous environments due to artifacts with that approach.

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================