Re: Pairinteractions

From: Ilya Chorny (
Date: Wed Aug 01 2007 - 17:09:41 CDT

I saw another posting on the list which explains that the energies in the
energy column correspond to the interaction energy. What I still do not
understand is what you would get if you ran this output with the dynamics
simulation. What if you want both the total interaction energy and the pair
interaction energy. Also what if you want more than two groups, such as
lipid self and protein lipid.



On 8/1/07, Ilya Chorny <> wrote:
> Hello,
> I would like to use pair interactions to monitor the self energy of my
> lipid as well as the interaction energy between the protein and the lipid. I
> am post processing the data in my dcd file using NAMD as shown in the
> manual. The only thing I don't understand, and this may be a stupid
> question, is what do I due with the force output? I need energies. Is there
> some obvious way to get the interaction energy from the forces. I apologize
> a priori if there is an obvious answer to my question
> Best,
> --
> Ilya Chorny Ph.D.

Ilya Chorny Ph.D.

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