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 <[email protected]> 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: [email protected] or [email protected] > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
