From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Aug 02 2007 - 21:36:28 CDT
Hi Ilya,
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
look.
Best,
Peter
> Thanks,
>
> llya
>
>
> 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
> 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* < ichorny_at_gmail.com
> <mailto: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
> 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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