Re: [AMBER] NaN error in .rst files - A request for some 'Clarity'

From: Ross Walker <>
Date: Thu, 27 Jan 2011 18:26:48 -0800

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

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| | |
| Tel: +1 858 822 0854 | EMail:- |

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Received on Thu Jan 27 2011 - 18:30:03 PST
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