From: Daniela Rivas (dani.rivas.r_at_gmail.com)
Date: Tue Jul 28 2015 - 09:45:07 CDT
Hi Chitrak,
That's the problem, I didn't put a restart frequency on my .conf file, I
forgot. I just set an xst and dcd frequency.
So, there's no way I can use the last trajectory saved on my output file?
Thank you,
Daniela.
2015-07-28 11:34 GMT-03:00 Chitrak Gupta <chgupta_at_mix.wvu.edu>:
> Hi Daniela,
>
> I am slightly surprised that NAMD did not create the restart files for
> you. What did you set your restart frequency as?
>
>
> Chitrak.
>
> On Tue, Jul 28, 2015 at 12:03 AM, Felipe Merino <
> felipe.merino_at_mpi-dortmund.mpg.de> wrote:
>
>> Hi Daniela,
>>
>> If you don't have the velocities for the configuration that you want to
>> restart from (either restart.vel or a velocity trajectory) then you have to
>> go from scratch.
>>
>> Felipe
>>
>>
>> On 28/07/15 02:21, Daniela Rivas wrote:
>>
>> Hi Chitrak,
>>
>> Thank you, but the problem is I can't find those restart files. It
>> seems like I forgot to add that line on my conf file. So, I want to know if
>> it's possible to retake my simulation just using the output.dcd file,
>> that'd be the only way, otherwise I'll have to run my dynamics all over
>> again :(
>>
>> Thanks,
>> Daniela.
>>
>> 2015-07-27 14:29 GMT-03:00 Chitrak Gupta <chgupta_at_mix.wvu.edu>:
>>
>>> Hi Daniela,
>>>
>>> Yes, you can. In fact it is fairly simple. NAMD should have created
>>> the restart files, specifically, the *.res.coor, *.res.vel and *.res.xsc
>>> files which contain, respectively, coordinates, velocities, and periodic
>>> box information. When you restart your simulation, make sure you read these
>>> files (the manual should explain how to do this). Remember to not specify a
>>> temperature as this is already being read from the *.vel file (I am
>>> assuming a constant temperature run. If that's not what you were doing,
>>> refer to the manual on how to restart that). Also, if you want the steps to
>>> be numbered from where it last crashed, use the "firsttimestep" option.
>>>
>>>
>>> Hope this helps,
>>> Chitrak.
>>>
>>> On Mon, Jul 27, 2015 at 11:32 AM, Daniela Rivas <dani.rivas.r_at_gmail.com>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> It's my first time using Namd and I don't know how to continue my
>>>> interrupted molecular dynamics simulation (electricity went off during the
>>>> weekend). I have my output.dcd and output.xst files and also have the log
>>>> file, so I know where to start again, I just don't know how to do it.
>>>>
>>>> Is there a way I can retake the simulation from the last point saved
>>>> in the output?
>>>>
>>>> I hope someone can help me :)
>>>>
>>>> Thanks,
>>>> Daniela.
>>>>
>>>
>>>
>>
>> --
>> Felipe Merino
>> Max Planck Institute for Molecular Physiology
>> Department of Structural Biochemistry
>> Otto-Hahn-Str. 11
>> 44227 Dortmund
>> Phone: +49 231 133 2306
>>
>>
>
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