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
