[gmx-users] Is My NPT Density High?

[Justin Lemkul]

On 3/27/17 3:28 PM, Jonathan Saboury wrote:
> Hello all,
>
> I have a system with a protein, lipid bilayer, and water/ions. I am getting
> a density of
> 1034 kg/m^3. I would have expected it to be lower because of the lipids. Is
> this a reasonable density for such a system?
>

An overall density of such a heterogeneous system is not useful or meaningful. 
Get a density profile as a function of z using gmx density.  The headgroup 
region can be especially tightly packed.

-Justin

> Image of system: http://oi64.tinypic.com/35jaykl.jpg
> NPT_density.xvg: https://pastebin.com/raw/UPZiRf1t
>
> If you need any other info please let me know, thank you!
>
> - Jonathan
>

-- 
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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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