[gmx-users] GMX Density – Setting Start and End Position Along Z Axis

[Justin Lemkul]

On 7/5/16 10:27 AM, ALEXANDER DHALIWAL wrote:
> Hello:
>
> I am attempting to use the gmx density function to calculate the electron
> density of a bilayer system with and without a solute. In order to do this,
> I must calculate the density of various elements (i.e., lipid head groups,
> lipid tails, solvent molecules) along the bilayer normal (z axis) for both
> a pure bilayer system that I have run and a similar one containing the
> solute, and then I must find the difference between the respective electron
> density profiles. However, each system has slightly different box
> z-dimensions, so the two instances of running the gmx density command
> result in differently spaced intervals along the axis. This makes it hard
> to compute the difference.
>
> Is there a specification by which I can choose the starting and ending
> place along the z-axis for my density calculation, such that I can have
> even intervals spaced at the same places for both of my calculations? I
> have tried changing the number of slices to approximately accommodate for
> the differences, but it still isn't working. Any help would be appreciated.
>

The density relative to the bilayer center is much more useful than trying to 
manipulate the box directly.  This is what the -center and -symm options are 
for.  See the complete description in the help text.  Centering on the bilayer 
itself in each case should resolve your problem.

-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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