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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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