On 2/14/12, leila karami <karami.leila1.gmail.com> wrote:
> Dear David A Case
>
> Thanks for your attention
>
>
> Both of serial and parallel jobs are ok. I use parallel run for free
> energy (TI).
>
> I did minimization step truely (imin=1) and now, I want to do
> equilibration step (imin=0).
>
> I attached input files (equilibration step of TI) to this e-mail.
>
> command uesd:
>
> mpirun -np 4 /home/md/amber10/bin/sander.MPI -ng 2 -groupfile
> free_1_ex_0.1.group &
>
>
> Best regards.
>
>
> On 2/13/12, David A Case <case.biomaps.rutgers.edu> wrote:
>> On Mon, Feb 13, 2012, leila karami wrote:
>>>
>>> I tried with icfe=0
>>
>>
>>>
>>> input file:
>>>
>>> free_1_eq_v1
>>> &cntrl
>>> imin = 0, ntx = 1, irest = 0,
>>> ntpr = 2500, ntwr = 2500, ntwx = 0,
>>> ntf = 2, ntc = 2,
>>> ntb = 2, cut = 10.0,
>>> nstlim = 250000, dt = 0.002,
>>> temp0 = 300.0, ntt = 3, gamma_ln = 5,
>>> ntp = 1, pres0 = 1.0, taup = 0.2,
>>> /
>>>
>>>
>>> Again, the job stopped, in NSTEP = 1.
>>
>> Assuming (although I'm not sure you have really stated this in any email)
>> that the serial and parallel tests run OK:
>>
>> You need to make as *simple as possible* a run with your system. Serial
>> job
>> only, icfe=0, nstlim=10, ntpr=1 (this is important!), ntb=1, ntp=0. You
>> should probably try imin=1 instead of 0. Don't use any queuing system;
>> take
>> care that you are not losing any error messages. The idea is to get
>> *some*
>> job (any job) to run with your prmtop and inpcrd files. Then you can
>> slowly
>> increase the complexity.
>>
>> If you still can't figure anything out, please post the prmtop and inpcrd
>> files.
>>
>> ...dac
>>
>>
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>
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Received on Mon Feb 13 2012 - 23:30:02 PST
