Re: Average energy in NAMD

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sun Jun 01 2008 - 21:02:40 CDT

Sorry, you're right! I meant namd plot.

http://www.ks.uiuc.edu/Research/vmd/plugins/namdplot/

On Jun 1, 2008, at 7:22 PM, Axel Kohlmeyer wrote:

> On Sun, 1 Jun 2008, JC Gumbart wrote:
>
> JCG> You could use NAMD Energy to output the relevant values to a
> file and then
> JCG> use any of a variety of scripting methods (tcl, perl, awk,
> etc.) to average
> JCG> them, or even a program like Excel.
>
> doesn't "namdenergy" run NAMD again?
> so why not parse and average the log directly?
>
> a.
>
> JCG>
> JCG> See here: http://www.ks.uiuc.edu/Research/vmd/plugins/namdenergy/
> JCG>
> JCG> On Jun 1, 2008, at 4:31 PM, feng jack wrote:
> JCG>
> JCG> >Hi, all,
> JCG> > I am new NAMD guy. I have some questiones about average
> energy:
> JCG> > There are three energy items in the standard output
> files: TOTAL,
> JCG> >TOTAL2
> JCG> >and TOTAL3, it seems that all of them are current energy
> rather than
> JCG> >average
> JCG> >energy. How can I obtain the average energy (e.g, if I want
> to obtain the
> JCG> >average energy in the last 200000 steps)?
> JCG> > Thank you for your patient.
> JCG> >
> JCG> > Best,
> JCG> > Jack
> JCG> >
> JCG> >
> JCG>
>
> --
> ======================================================================
> =
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://
> www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA
> 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> ======================================================================
> =
> If you make something idiot-proof, the universe creates a better
> idiot.

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