[gmx-users] High density

[Justin Lemkul]

On 5/23/15 10:43 PM, Vy Phan wrote:
> Dear all,
> My system includes protein and spc water.
> After running 1000ps NPT equilibrium I got the density is 1010+/-1.25.
> I hope I can get the density is 1000kg/m3. I run for a long  NPT step, I
> still get around 1010.
> Is this value is fine ? Do I need to run more?
>

The density you get won't match the bulk water density because (1) your system 
isn't pure water and (2) the SPC model doesn't match experimental density exactly.

-Justin

-- 
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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

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