Hi,
Why do you think there is something wrong? The absolute value of the
energy doesn't tell you much - what matters are differences in energy.
In general, the value of each energy term will grow as the number of
atoms increases. Also remember also you're only looking at 2
components of the energy function. There are many other components
which may be important to your system (like solvent energy).
-Dan
On Mon, Apr 24, 2017 at 11:07 PM, Aishani Prem <aishaniprem.gmail.com> wrote:
> Hi,
> I am using 'pairwise' to calculate the van der waals and electrostatic
> energy between the backbone atoms in my proteins.
> My input file looks like:
> trajin pdb_md1_.mdcrd
> pairwise :1-56.N,CA,C,O out energy.out time 0.1
>
> and I run the command :
> $AMBERHOME/bin/cpptraj -p pdb_vac.prmtop -i vdwaal.trajin
>
> The energy values that I get in my output file is unexpectedly high
> (~84000kJ/mol) when I add in the backbone atoms in the mask. Is there
> anything wrong with the calculations?
>
> --
> Thank You and Regards,
> Aishani Chittoor Prem
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Apr 25 2017 - 07:00:02 PDT
