Hi Ross,
I will also do these tests (just short MDs cca 50 000 steps might be
enough I think) soon,
and I will let here know the results.
Best,
Marek
Dne Fri, 28 Jan 2011 03:26:48 +0100 Ross Walker <ross.rosswalker.co.uk>
napsal/-a:
> Hi All,
>
> I am hoping to be able to get some clarity for this thread so that we can
> start to look at what might actually be going on here. Right now there
> are a
> lot of theories but no real concrete examples to back things up.
> Specifically I would appreciate it if someone who sees this NAN problem
> could take their simulation and run the following:
>
> 1) NTT=3, NTB=2 - This one we already know the problem exists.
>
> 2) NTT=3, NTB=1 - This is NVT and will rule out the barostat if the
> problem
> still exists.
>
> 3) NTT=1, NTB=2 - This is NPT but NOT using the random number stream. If
> this crashes it means the problem is likely in the barostat rather than
> the
> random number stream.
>
> 4) NTT=1, NTB=1 - This is NVT not using the random number stream. If this
> crashes then both my theories are wrong.
>
> 5) NTT=0, NTB=1 - This is NVE, if this crashes then we are in a whole
> world
> of pain...
>
> I want to find out specifically which simulation modes show problems and
> which do not. I am 'hoping / assuming' that the problem is restricted to
> either NPT calculations or Langevin simulations or possibly NPT with
> Langevin. However, I need someone to carefully try these options and
> document the issue. Everyone's help is greatly appreciated.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
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Received on Fri Jan 28 2011 - 02:00:02 PST
