There is a mdin variable for setting the frequency of writing it, maybe
ntwr, but check.
Bill
On 7/4/17 9:33 AM, Núbia Prates wrote:
> 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
>>>>
>>>> _______________________________________________
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Received on Tue Jul 04 2017 - 10:00:03 PDT
