Re: NAMD Run Instabilities

From: Axel Kohlmeyer (
Date: Mon Sep 10 2012 - 08:28:17 CDT

> 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 and
> 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 out
>> > 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
>> 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
International Centre for Theoretical Physics, Trieste. Italy.

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