Re: Pairinteractions

From: Ilya Chorny (
Date: Thu Aug 02 2007 - 12:24:14 CDT

By Total interaction energy I mean the potential energy of the system. If I
wanted to output the the total potential energy of the system and at the
same time the pair interaction energy between two subparts of the total
system, would I be able to do that?

A second question, when I ran the post process to calculate the Lipid self
potential energy. I got the same values as the production run which outputs
the potential energy of the system. Also the vDW forces were zero and
electrostatic were very small. My protein is fixed to its original atomic
position and the membrane phosphate is constrained in the normal dimension.
I also have unconstrained water in the system. It's not clear to me why the
self energy outputs are the same values as the total potential energy of the
system. Any thoughts?



On 8/1/07, Peter Freddolino <> wrote:
> Hi Ilya,
> you're correct that in a postprocessing run, the energy shown
> corresponds to that of the groups you've selected for interaction
> calculation. It is usually better in practice to use pairinteractions
> only during postprocessing; you should get the total energies from the
> production run. I don't know what difference you see between "total
> interaction energy" and "pair interaction energy" -- what are you
> thinking of here? To work with more than two groups, you need to perform
> separate postprocessing calculations for each pair (or self) interaction.
> Best,
> Peter
> Ilya Chorny wrote:
> > 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.
> >
> > Thanks,
> >
> > Ilya
> >
> >
> > 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.

Ilya Chorny Ph.D.

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