From: Marc Gordon (marcgrdn55_at_gmail.com)
Date: Mon Sep 10 2012 - 08:39:55 CDT
Sorry That was the extreme end of my messing around to see at what points
the instabilities were cropping up on. I perhaps shouldn't have bothered to
include the run part as that has varied widely from test to test. I think
the biggest duration I tried was something like 2000ns and not just 1500ns.
At more reasonable numbers of steps (anything below 800ns if I recall
correctly) the system is actually pretty stable and I don't see the
instabilities. It is only when I get to numbers of steps close to a billion
that it starts with the instability.
The reason I started cranking the run durations up was that my supervisor
pointed out that the free energy plots being produced were varying between
identical runs and were a little jagged. She suggested that perhaps I had
an issue with convergence and to run it longer. So that is what I did.
Should I perhaps have tried a different tactic?
What do you mean by "the tiny size of the system make almost all of the
other discussions pointless. there is no way to make this kind of system
scale beyond a few threads."?
You mean I should keep my numsteps low? There is no need to crank it up so
high? This is where this instability is coming from?
On Mon, Sep 10, 2012 at 3:28 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> > As to atom numbers I don't have the structure files in front of me at the
> > moment but if memory serves it was 47 atoms. (I can check this for you
> > get a more precise number if this is important?). I'm guessing by the
> > standards you are used to in molecular dynamics that is a small number.
> by NAMD standards, 47 atoms is a ridiculously small number.
> that is a system size where almost all of the features in a code
> like NAMD that are added for better scaling will mainly add overhead.
> i also don't quite understand, what purpose that long
> a trajectory for such a small system serves.
> the tiny size of the system make almost all of the
> other discussions pointless. there is no way to make
> this kind of system scale beyond a few threads.
> >> > Any insights would be appreciated as right now I am tearing my hair
> >> > with
> >> > this problem.
> >> as usual, the usual reminder:
> >> it is difficult to discuss such problems on such a generic level.
> >> running an MD is a bit of a balancing act and debugging it is
> >> like being a medical doctor: the description of the patient is
> >> not necessary pointing to the real problem. the more details
> >> and tangible information is made available the better the diagnosis.
> >> otherwise there is not much more to say as in:
> >> "doctor, doctor. it hurts when i am doing this."
> >> "well, don't do it then."
> >> cheers,
> >> axel.
> >> --
> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> >> International Centre for Theoretical Physics, Trieste. Italy.
> > Yes I have noticed this. This is pretty much my first study involving
> > molecular dynamics and I found that on my local machine it took quite a
> > while before I found config settings that worked.
> > Any details you think might be helpful I will try to provide. Perhaps the
> > relevant portions of the config file:
> > binaryoutput yes
> > outputEnergies 100
> > dcdfreq 1000
> > exclude scaled1-4
> > 1-4scaling 1
> > COMmotion no
> > dielectric 1.0
> > switching on
> > switchdist 9
> > cutoff 10
> > pairlistdist 12
> > reassignFreq 1000
> > reassignTemp 25
> > reassignIncr 25
> > reassignHold 300
> > colvars on
> > colvarsConfig PhiPsiMetaDaDGlc-a12-aLRha_charmm.txt
> > run 1500000000
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
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