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

From: peker milas <pekermilas.gmail.com>
Date: Sat, 29 Jan 2011 14:59:51 -0800

Hi Ross and Marek,

As a quick update, i run three 1.5 ns simulations with my system. One
for NTT=3, NTB=1 case with ig=-1, one for NTT=1, NTB=2 with ig=-1 ,
and another one for NTT=1, NTB=2 without ig=-1. None of them produced
NaN s. I will continue with other 2 cases. I will let you know about
the results...

best
peker

2011/1/28 Marek Maly <marek.maly.ujep.cz>:
> 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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>>
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>
>
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Received on Sat Jan 29 2011 - 15:30:02 PST
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