Re: Pairinteractions

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Aug 02 2007 - 00:41:56 CDT

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.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:02 CST