From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Aug 02 2007 - 21:36:28 CDT
Ilya Chorny wrote:
> 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?
No; the best way to do this is take the total energies from the initial
run, and use a pairinteraction postprocessing calculation to get the
interaction energy you're interested in.
> 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?
That seems very odd, and shouldn't be the case. Note that the
interactions between pairs of fixed atoms should will *not* be included
in the reported energies, but that doesn't explain why you get the same
energies when the water is excluded. If you send your input I can have a
> On 8/1/07, *Peter Freddolino* <petefred_at_ks.uiuc.edu
> <mailto:petefred_at_ks.uiuc.edu>> 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
> separate postprocessing calculations for each pair (or self)
> 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
> > 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* < ichorny_at_gmail.com
> > <mailto:ichorny_at_gmail.com <mailto:ichorny_at_gmail.com>>> wrote:
> > Hello,
> > I would like to use pair interactions to monitor the self
> > of my lipid as well as the interaction energy between the
> > and the lipid. I am post processing the data in my dcd file
> > 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
> > output? I need energies. Is there some obvious way to get the
> > interaction energy from the forces. I apologize a priori if
> > is an obvious answer to my question
> > Best,
> > --
> > Ilya Chorny Ph.D.
> > --
> > Ilya Chorny Ph.D.
> Ilya Chorny Ph.D.
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