Re: [AMBER] NaN error in .rst files

From: Ross Walker <>
Date: Wed, 26 Jan 2011 22:59:31 -0800

BTW, to all those following this thread. I would like to know if anybody has
seen this NaN issue when running anything other than NTT=3. My hunch is that
somehow the pseudo random number generator is running out of valid random
numbers and starts handing out garbage. Weight can be added to this theory
if people are running NTP simulations with NTT=1 which will not use the
random number stream.

The alternative theory is that it is something related to the barostat. In
which case I would expect this problem to only show up with NTP simulations
and for NVT and NVE to work fine. So essentially I would like to know if
this problem is seen with any of the following combinations of settings:

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...

Thank you.

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 Wed Jan 26 2011 - 23:30:03 PST
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