[gmx-users] gmx distance - COM distance issue

[Justin Lemkul]

On 7/14/15 10:33 PM, Carlos Navarro Retamal wrote:
> Dear gmx users,
> In an attempt to analyse the interaction between a Protein and a Bilayer (in a CG MD simulations) i’m using gmx distance as following:
> gmx distance -f DFMG-200ns.xtc -s DFMG-200ns.tpr -n index.ndx -select 'com of group "Protein" plus com of group "Membranes"' -oall distance.xvg.
> By analysing the CONTACTS between both macromolecules i now that the protein interact peripherally with the membrane (moving from the aqueous solution to the membrane), by interacting with the head group of the bilayer. My problem is that, contrary to what i might imagine, base on the ‘distance’  analysis i’m seeing that the distance between the molecules increase during time:
> beginning:
>        0.000    4.062
>      100.000    3.952
>      200.000    3.768
>      300.000    3.576
>      400.000    3.422
>      500.000    3.526
>      600.000    3.561
>      700.000    3.619
>      800.000    3.643
>      900.000    3.682
>
> end:
>   199100.000    5.347
>   199200.000    5.244
>   199300.000    5.273
>   199400.000    5.410
>   199500.000    5.369
>   199600.000    5.275
>   199700.000    5.415
>   199800.000    5.525
>   199900.000    5.557
>   200000.000    5.441
>
> I tried using the -pbc flag (when i used gmx distance) without luck (i got the same values as before).
> What could be the reason?

Because only the vertical dimension (presumably z here in the case of a 
membrane) is relevant.  The protein can still be peripherally associated at a 
"corner" of the box, which would have a large COM distance but small z 
component, indicating binding.  Use -oxyz instead of -oall.

-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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