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

[Justin Lemkul]

On 7/5/16 1:18 PM, ALEXANDER DHALIWAL wrote:
> 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.
>

Can you provide an image that illustrates your problem?  I can't visualize how 
the problem is arising.  If the bilayer is the same, centering on it should 
remove any issue associated with different box sizes; the position relative to 
the center should be similar.  Maybe I'm just missing something here that is 
specific to the setup of your system.

> 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
>

Help info can be printed directly by every tool, e.g. gmx help density or gmx 
density -h.

-Justin

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

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

==================================================