[gmx-users] gmx distance - COM distance issue

[V.V.Chaban]

Maybe your protein is not spherical enough to benefit from the
center-of-mass-based analysis? Furthermore, was your initial system
configuration properly equilibrated?




On Tue, Jul 14, 2015 at 11:33 PM, Carlos Navarro Retamal
<cnavarro at utalca.cl> 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?
> Thanks in advance,
> 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
>
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