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

[ALEXANDER DHALIWAL]

Hi Justin,

Thank you for such a prompt reply. I am currently using the -center option
in my density calculation; an example of my code is:

gmx density -f md_1_5_cat.trr -s md_1_5_cat.tpr -ei electrons.dat -n
popc_densities.ndx -o test.xvg -center
...
Select the group to center density profiles around: Group 2 (POPC)
Select 1 group to calculate density for: Group 5 (SOL)

However, the output when run for two different system generates equally
spaced intervals that don't necessarily line up. So, when I want to
evaluate the difference at, say, the peak of the electron density map, the
z-values between my two maps do not correspond. I believe that if I could
specify the number of slices using the -sl designation and specify the
bounds that I need for the density calculations, each of my .xvg density
files would have the same z-coordinates between them, and their differences
could be directly evaluated. Is this possible? No combination of using
-center, -symm, and -relative so far has helped me achieve this yet.

Additionally, I am currently using the following link to inform me on
different gromacs functions. Is it possible to receive more information on
these functions besides sifting through archived emails?

http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/onlinehelp/gmx-density.html

Thanks again!

– Alex

On Tue, Jul 5, 2016 at 12:55 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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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