Re: [AMBER] difference of distances using cpptraj in free energy plot

From: Daniel Roe <>
Date: Wed, 12 Sep 2018 13:55:23 -0400


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
distance D1 <options>
distance D2 <options>
rmsd R1 <options>
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,


On Wed, Sep 12, 2018 at 8:07 AM Nisha Amarnath Jonniya
<> 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

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Received on Wed Sep 12 2018 - 11:00:04 PDT
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