Thank you for the information.
On Wed, 12 Sep 2018, 11:27 pm Daniel Roe, <daniel.r.roe.gmail.com> wrote:
> 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
>
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Received on Thu Sep 13 2018 - 01:00:02 PDT
