[gmx-users] Re: clarification regarding contact map - g_mdmat

[Kavyashree M]

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 <hmkvsri at 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
>
>