Dear users, Sorry. It is because the unit of the cutoff distance ]is in nm.
Thank you kavya On Fri, Feb 1, 2013 at 1:28 PM, Kavyashree M <hmkv...@gmail.com> wrote: > Dear users, > I used g_mdmap to calculate the C-alpha contact map of > the trajectory. the distance cut off of 8.0 Ang was selected > The protein is a dimer of 237 residues. The output of -no was > like this - > #res ratio tot mean natm mean/atm > 1 1.000 473 473.000 1 473.000 > 2 1.000 473 473.000 1 473.000 > 3 1.000 473 473.000 1 473.000 > 4 1.000 473 473.000 1 473.000 > 5 1.000 473 473.000 1 473.000 > 6 1.000 473 473.000 1 473.000 > 7 1.000 473 473.000 1 473.000 > .... > So it mean that on an average each calpha atom contacts all > other C-alpha atom in the whole trajectory at some point of time. > > In order to cross check it I collected data only for one time frame. > This was also very similar results. all the residues have a minimum > of atleast 471 contacts. > > Some one kindly clarify where I am going wrong.? the command > I used was - > g_mdmat -f .*.xtc -s *.tpr -no *.xvg -mean *.xpm -b 4000 -e 4000 -t 8.0 > > Is this trucating distance in Angstroms or nanometer? > > Thank you > Kavya > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
