[gmx-users] vaccume simulation

Justin Lemkul jalemkul at vt.edu
Mon Aug 31 13:34:38 CEST 2015

On 8/31/15 7:01 AM, tasneem kausar wrote:
> Dear gmx-users
> I am trying to calculate rmsd for protein backbone. I have done simulation
> in vacuum. There are for negative charges in the system. During solvation
> via genbox, 4 water molecule were added using -maxsol. The charges have
> been neutralized by addition of 4 Na ion and water molecules were replaced
> by these ions. Then after minimization I have run full md for 50 ns.
> if there is any other way to neutralize the charge in vacuum, please tell.
> Is the way I have opted for vavuum simulation right?

I don't see why you would do this.  The ions probably just fly away and serve no 
functional purpose.



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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