[gmx-users] Regarding creating a box around the molecule and neutralization of charge before EM and MD
jalemkul at vt.edu
Fri Jul 21 23:18:23 CEST 2017
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 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
More information about the gromacs.org_gmx-users