Hello,
On Mon, Mar 29, 2010 at 9:40 PM, Yang Li <chlorin316.hotmail.com> wrote:
>
> Hi,
> I took Dr. Case's recommendation and run a 10 step simulation. The test case did not pass, it was running and I tried to tail -f the .out file, but nothing showed up. The simulation ran for the entire weekend and there's no output file so I stopped it.
> What do you think the problem is?
I'm not quite sure what you're doing here, but I have a guess. If I'm
wrong, then listen to Dan's email. However, if you're using your
topology file and coordinate file with your input file, these are not
the pre-packaged test cases. To see if the test cases pass, go to the
directory $AMBERHOME/test, set the environment variable DO_PARALLEL to
whatever you use to call mpi programs and run "make test.parallel" in
that directory.
Do the tests pass? If so, try changing your input file parameters to
match the test cases until it works. I'm guessing that your input
file has an inconsistency that's not caught.
Good luck!
Jason
>
>
> With regards,
> Yang
>
>> From: carlos.simmerling.gmail.com
>> Date: Mon, 29 Mar 2010 15:58:40 -0400
>> Subject: Re: [AMBER] simulation under pressure
>> To: amber.ambermd.org
>>
>> have the test cases passed? is the job still getting CPU time? do you get
>> any output at all?
>>
>> On Mon, Mar 29, 2010 at 3:53 PM, Yang Li <chlorin316.hotmail.com> wrote:
>>
>> >
>> > Hi, Dr. Case,
>> >
>> > Thank you for you recommendations. I checked and my prmtop was
>> > periodic and solvated. I tried to run a 10 step simulation, here is my
>> > input file.
>> >
>> > DNA 12-ATmer simulation under 100atm
>> > &cntrl
>> > imin = 0, irest = 1,
>> > igb = 0, ntx = 5,
>> > ntt = 3, gamma_ln = 1.0,
>> > tempi = 300.0, temp0 = 300.0
>> > ntp = 1, taup = 2.0, pres0 = 100,
>> > ntb = 2, ntc = 2, ntf =2,
>> > nstlim = 10, dt = 0.01
>> > ntwx = 1, ntpr =1
>> > cut = 12.0
>> > /
>> >
>> >
>> > However, the simulation has run for the entire weekend again and did
>> > not finish on the 3G processor.
>> >
>> > Please let me know what I can do.
>> >
>> >
>> > With regards,
>> >
>> > Yang
>> > _________________________________________________________________
>> > Check your Hotmail from your phone.
>> >
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>> >
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>
> _________________________________________________________________
> Check your Hotmail from your phone.
> http://go.microsoft.com/?linkid=9712957_______________________________________________
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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 Mon Mar 29 2010 - 21:00:03 PDT
