Bill,
I am trying to write the rst file, as you suggested, using the command:
sander -O -i min_rest.in -o rest.out -p .prmtop -c .rst -r rest.rst -ref .rst
But the rst file is not written! What Am I doing wrong?
Nubia
________________________________
De: Bill Ross <ross.cgl.ucsf.edu>
Enviado: terça-feira, 4 de julho de 2017 12:01
Para: amber.ambermd.org
Assunto: Re: [AMBER] How continue a crached minimization step?
Nubia,
If you have power problems, the solution is to write the restrt file
frequently enough so that a machine crash doesn't hurt too much. If you
didn't write one in your ~22 hours of run time, the best you can do is
be prepared the next time.
Bill
On 7/4/17 7:24 AM, Núbia Prates wrote:
> Bill,
>
>
> Actually I am heaving problems with blackout. I want to continue the equilibration where it stopped.
>
> I have attached the .in and mdinfo files.
>
>
> Nubia
>
>
> ________________________________
> De: Bill Ross <ross.cgl.ucsf.edu>
> Enviado: segunda-feira, 3 de julho de 2017 17:50
> Para: amber.ambermd.org
> Assunto: Re: [AMBER] How continue a crached minimization step?
>
> It sounds like your machine didn't crash, your simulation did?
>
> If you are having problems with a simulation getting started, best to
> paste the .in file (might as well start with the minimization) into your
> mail, along with the part of the output indicating failure.
>
> Bill
>
>
> On 7/3/17 12:11 PM, Núbia Prates wrote:
>> Thank you Elvis and Bill,
>>
>>
>> Now I am heaving the same trouble during the equilibration.
>>
>> Can you help me with that?
>>
>>
>> Best
>>
>> Núbia
>>
>>
>> ________________________________
>> De: Bill Ross <ross.cgl.ucsf.edu>
>> Enviado: segunda-feira, 3 de julho de 2017 15:21
>> Para: amber.ambermd.org
>> Assunto: Re: [AMBER] How continue a crached minimization step?
>>
>> Usually minimization is not worth running at much length, if it is to
>> prepare for dynamics. I would try about 5-30 minutes of wallclock time
>> total, so a crash shouldn't matter. Plot the total energy to see what I
>> mean.
>>
>> Bill
>>
>> On 7/3/17 7:38 AM, Núbia Prates wrote:
>>> Hello,
>>>
>>> I was running a minimization, but it was not completed due to lack of power. I was wonder if it is possible to continue minimizing where it stopped or I have to do another?
>>>
>>>
>>> Best
>>>
>>> Núbia
>>>
>>> _______________________________________________
>>> AMBER mailing list
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Received on Tue Jul 04 2017 - 10:00:03 PDT
