From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Oct 24 2013 - 11:53:37 CDT
> -----Ursprüngliche Nachricht-----
> Von: Norman Geist [mailto:norman.geist_at_uni-greifswald.de]
> Gesendet: Donnerstag, 24. Oktober 2013 18:52
> An: 'Jim Phillips'
> Cc: Namd Mailing List (namd-l_at_ks.uiuc.edu)
> Betreff: AW: namd-l: Re: DEVELOPER QUESTION -> NAMD Internal energy
> unit and TCL interface
> Thank you for your interest. The problem is as follows:
> I adapted the replica.namd script to run $steps_per_run-$somesteps.
> Then there's a loop that does "run 1" * $somesteps to fill up the rest
> of $steps_per_run. Inbetween the "run 1" im using the "save_array"
> command to get the current energies. All this is done with
> stepspercycle/fullelectfrequency/nonbondedfreq = 1. Now the weird thing
> is that the potential energies I get between the "run 1" are about 9
> times higher until a interval of outputenergies is hit. So as
> replica.namd sets output energies to $steps_per_run/10 my energies are
> huge (about 104000) for 9 steps and the last one that fills the 10 is
> comparable to the ones that get printed to the logfile (about 1500).
Forgot to mention the example regards on $steps_per_run = 100
> That’s the reason I supposed that namd transforms the values before
> writing them to the log and that as long there's no need to output
> them, it stores them in some computational optimized manner. I hope I
> explained better now and that you know what I'm talking about. I need
> to know what exact factor is in there, or why this "mysterious"
> save_array command where I have no idea where it gets the values from,
> outputs that weird numbers.
> Thanks a lot
> Norman Geist.
> > -----Ursprüngliche Nachricht-----
> > Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> > Auftrag von Jim Phillips
> > Gesendet: Donnerstag, 24. Oktober 2013 17:02
> > An: Norman Geist
> > Cc: Namd Mailing List
> > Betreff: namd-l: Re: DEVELOPER QUESTION -> NAMD Internal energy unit
> > and TCL interface
> > On Thu, 24 Oct 2013, Norman Geist wrote:
> > > I'm currently adapting some of the replica.namd TCL code. I
> > that
> > > the energies got through save_array output different values before
> > and after
> > > outputenergies took effect. Could it be that namd stores these
> > in a
> > > different unit and that the energies get transformed before printed
> > to the
> > > log? What's the exact factor here?
> > Energy is always kcal/mol. The outputEnergies setting also controls
> > how
> > often nonbonded (vdw and electrostatic) energies are calculated, so
> > want outputEnergies to be a multiple of fullElectFrequency and
> > steps_per_run to be a multiple of outputEnergies.
> > Beyond that I don't understand your question.
> > > Additionally, the procedure how to get these energy values isn't
> > documented
> > > very well. Are these values accessible from TCLforces, too, this
> > would save
> > > me from doing "run 1" what unfortunately comes with "stepspercycle
> > > "fullelectfrequency 1" and "nonbondedfreq 1".
> > Try "run 0" instead. It'll do one energy evaluation with no
> > integration.
> > We could make energies from the *previous* timestep available in
> > tclForces
> > (the way total forces on requested atoms are available now). This
> > would
> > provide the timestep synchronization that I think you're looking for.
> > Jim
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