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 |
>> ---------------------------------------------------------
>>
>> Note: Electronic Mail is not secure, has no guarantee of delivery, may
>> not
>> be read every day, and should not be used for urgent or sensitive issues.
>>
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> __________ Informace od ESET NOD32 Antivirus, verze databaze 5825
>> (20110127) __________
>>
>> Tuto zpravu proveril ESET NOD32 Antivirus.
>>
>> http://www.eset.cz
>>
>>
>>
>
>
> --
> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> http://www.opera.com/mail/
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jan 29 2011 - 15:30:02 PST
