If this works then the calculation is fine, they are different
but both reasonable trajectories. The same thing would
probably happen using two different kinds of computers.
cristian obiol wrote:
> Dear Carlos,
> Yes, I obtained the same energies in both queues setting ntpr=1,
> So it is a problem of roundoff errors of integration steps ?
> Thanks
>
> Cristian Obiol
> Biological Systems Modelling and Drug Design
> Research Group
> University of Barcelona
>
>
>
>
>
>
>
>
>> it might be easier to run 500 steps of MD and set ntpr to 1.
>> do they match? as Dave Case said in his reply, if the initial
>> forces are not too high, this should work.
>>
>> cristian obiol wrote:
>>
>>> Dear Carlos,
>>> The ntpr is set to 1000, my problem was that i killed the two jobs (4p
>>> 8p) in the first steps because i noticed that the error between the
>>> energies grew up,
>>> Now I carried out the jobs to the final and the errors only oscilates
>>> between 5 to 107 of 157,000 Kcal/mol and in an aleatory way.
>>> This variations in the total energy in 4/8 processors can be normal,
>>> I'm right ??
>>>
>>>
>>> Thanks in advance.
>>>
>>> Cristian Obiol
>>> Biological Systems Modelling and Drug Design
>>> Research Group
>>> University of Barcelona
>>>
>>>
>>>> in the third MD step (of ~1fs each) or third time that the
>>>> energy is written in the output (which could be longer)?
>>>> I get identical output for different # of cpus up to a few hundred
>>>> steps of 1fs each.
>>>>
>>>> cristian obiol wrote:
>>>>
>>>>> Dear AMBER users,
>>>>>
>>>>> We have running a cluster of 12 processors in linux Debian platform
>>>>> (mpich 1.2.6. and fortran intel_fc_80 compiler), and our results in
>>>>> sander8 outputs are different depending the queue (4 or 8) that we are
>>>>> using, around 0.0001 % in the final energy in the third step.
>>>>>
>>>>> We are disturbed because the test factor_ix for sander 8 is well passed
>>>>> in both queues.
>>>>>
>>>>> Any comments are welcome,
>>>>> Thanks in advance.
>>>>>
>>>>> Cristian Obiol
>>>>> Biological Systems Modelling and Drug Design
>>>>> Research Group
>>>>> University of Barcelona
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Received on Sun Feb 26 2006 - 06:10:10 PST
