Sorry again---he correct output is simply what is pasted in the main text of
the *email*.
On Wed, Jun 15, 2011 at 2:24 PM, Erin Kelly <erkelly4572.gmail.com> wrote:
> Sorry that BATCH_ERRORS file is incorrect from a previous run; the correct
> output is simply what is pasted in the main text of the file. Sorry for the
> confusion.
>
> I should mention that these simulations fail immediately when I submit
> them, I don't even have time to see it listed in the job que, so I'm not
> sure that shorter runs would help.
>
> Erin
>
>
> On Wed, Jun 15, 2011 at 2:15 PM, David A Case <case.biomaps.rutgers.edu>wrote:
>
>> On Wed, Jun 15, 2011, Erin Kelly wrote:
>> >
>> > I've been attempting to complete "Tutorial 1: Molecular dynamics
>> simulation
>> > of protein" with 3OGP.pdb I was able to make it through the
>> minimizaton,
>> > heating, and equilibration steps but was stopped at the production step.
>> I
>> > was given the following error in an BATCH_ERROR file:
>>
>> The output file says this:
>>
>> peek_ewald_inpcrd: SHOULD NOT BE HERE
>>
>> This indicates that the program could not process your inpcrd file
>> (3OGP_equil.rst) correctly. Are you sure that this is really a restart
>> file
>> from a previous MD (not minimization) run? Is there any chance that your
>> file
>> naming scheme got mixed up, or something like that?
>>
>> It's worth running a very short attempt with the serial code, just to rule
>> out any parallel problems, but you will probably see the same error.
>>
>> Look at the inpcrd file, especially the last few lines (you might want to
>> post
>> those). Compare to a restart file from some run that works.
>>
>> [In the BATCH_ERRORS file you posted, there is an addition message:
>>
>> Unit 5 Error on OPEN: prod.in
>>
>> This would indicate that the program could not even find the prod.infile.
>> But since it is reprinted in the output file, it guessing(!!?!) that this
>> is
>> the BATCH_ERRORS file from some other run. When you have problems, try a
>> short interactive run so that errors and warnings don't get lost or
>> confused
>> with earlier errors, and so on.]
>>
>> ...good luck....dac
>>
>>
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>
>
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Received on Wed Jun 15 2011 - 12:30:06 PDT
