Hi,
CPPTRAJ can do some math with data sets. So e.g. if your distances are
stored in data sets named D1 and D2 and your RMSD is in R1:
parm myparm.parm7
trajin mytraj.nc
distance D1 <options>
distance D2 <options>
rmsd R1 <options>
run
Delta = D1 - D2
hist R1,*,*,*,100 Delta,*,*,*,100 <other options>
Note here I'm choosing 100 bins for X and Y but other things may work
better. Also note if the data is already generated you can read it in
with the 'readdata' command.
Hope this helps,
-Dan
On Wed, Sep 12, 2018 at 8:07 AM Nisha Amarnath Jonniya
<phd1601271002.iiti.ac.in> wrote:
>
> Dear Amber users,
>
> I have a query regarding free energy plot with rmsd on x-axis and
> difference of two distances on y-axis (D1-D2), where D1 is the distance
> between two residues say Lys-Glu and D2 is another distance say Glu-Arg. So
> how to calculate this differences of the distance using CPPTRAJ for free
> energy plot.
>
>
>
>
> --
>
> Nisha Amarnath Jonniya
> PhD Research Scholar
> Biosciences and Biomedical Engineering
> Indian Institute of Technology, Indore
> India
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 12 2018 - 11:00:04 PDT
