[gmx-users] gmx distance - COM distance issue

[Carlos Navarro Retamal]

Hi Justin,
First of all, thanks a lot for your reply.
I saw during the simulation that; indeed, the protein positioned in a corner of the simulation box, so i ‘refined’ the trajectory by centering the protein.
And now, the gmx distance method gave me more ‘logical’ distances with respect the adsorption process of the protein into the bilayer.
Thanks a lot.
Best,
Carlos

--
Carlos Navarro Retamal
Bioinformatics Engineering
Ph. D (c) Applied Sciences.
Center of Bioinformatics and Molecular Simulations. CBSM
University of Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 712201 798
E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl



On July 15, 2015 at 10:28:42 AM, Justin Lemkul (jalemkul at vt.edu<mailto:jalemkul at vt.edu>) wrote:


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

--
==================================================

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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