From: Ilya Chorny (ichorny_at_gmail.com)
Date: Thu Aug 02 2007 - 15:47:23 CDT
Does NAMD energy let you decompose the energy into pair interactions?
On 8/2/07, Richard Wood <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
>
>
> ----- Original Message ----
> From: Ilya Chorny <ichorny_at_gmail.com>
> To: Peter Freddolino <petefred_at_ks.uiuc.edu>
> Cc: 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> 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>> 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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