Re: Pairinteractions

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Aug 02 2007 - 21:37:16 CDT

NAMDenergy is really just a gui for making and running pair interaction
calculations, so yes. Might be worth trying what you were doing before
in namdenergy to see if you get the same result.
Peter

Ilya Chorny wrote:
> Does NAMD energy let you decompose the energy into pair interactions?
>
> On 8/2/07, *Richard Wood* <rwoodphd_at_yahoo.com
> <mailto:rwoodphd_at_yahoo.com>> wrote:
>
> Can't one use VMD and the NAMDenergy plugin to do this?
>
> Richard
>
> Richard L. Wood, Ph. D.
> University of Minnesota
> Dept. of Medicinal Chemistry,
> College of Pharmacy
> 717 Delaware St. SE
> Minneapolis, MN 55414-2959
> rwoodphd_at_yahoo.com <mailto:rwoodphd_at_yahoo.com>
>
>
> ----- Original Message ----
> From: Ilya Chorny < ichorny_at_gmail.com <mailto:ichorny_at_gmail.com>>
> To: Peter Freddolino <petefred_at_ks.uiuc.edu
> <mailto:petefred_at_ks.uiuc.edu>>
> Cc: namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>
> Sent: Thursday, August 2, 2007 12:24:14 PM
> Subject: Re: namd-l: Pairinteractions
>
> 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?
>
> 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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> Ilya Chorny Ph.D.

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