[gmx-users] gmx distance - COM distance issue

Carlos Navarro Retamal cnavarro at utalca.cl
Wed Jul 15 04:33:29 CEST 2015

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:
      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

 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?
Thanks in advance,
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

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