On Fri, Mar 5, 2010 at 11:06 PM, Imtiaz Shafiq <imtiazshafiq.gmail.com> wrote:
> Dear Ramesh,
>
> This may not answer your question, but I am asking out of curiosity that you are using -np 18 i mean 18 processors. Should not it be to processors equal to Power of 2 for sander.MPI
A power of 2 will use a different (more efficient) algorithm in
sander.MPI. This is not true for pmemd. However, the results should
still be the same (just a little slower).
Good luck!
Jason
>
> Regards
> Imtiaz
>
>
>
> On 6 Mar 2010, at 03:54, kureeckal ramesh wrote:
>
>> Hi AMBER users,
>>
>> I was successful in completing the TrpCage tutorial using AMBER 10 (running in cluster) and was also able to complete the MD analysis for the same.
>> Now, I have started working with my sample protein ( ab-initio prediction) and was able to complete only upto heating stage. In the production stage (comprising a total of 10 stages with 5 ns / stage; i. e total of 50 ns simulation), the program got "TERMINATED" after the completion of 1st stage. AT the begining of the 2nd stage, following error is reported:
>>
>> -----------------------------------------------------------------------------------------------------------
>> mpirun -np 18 /usr/local/amber10/exe/sander.MPI -O -i equil.in -p FT.prmtop -c
>> equil1.rst -r equil2.rst -o equil2.out -x equil2.mdcrd
>> At line 237 of file _getcor.f
>> Fortran runtime error: Bad value during floating point read
>> ---------------------------------------------------------------------------------------------------------------
>>
>> I request you to kindly guide me in overcoming this problem
>>
>>
>> With the best of regards
>> Ramesh K V
>>
>>
>>
>> The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/
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>
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--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Mar 05 2010 - 21:00:03 PST
