Re: Interrupted Molecular Dynamics Simulation

From: Purushottam Dixit (dixitpd_at_gmail.com)
Date: Tue Jul 28 2015 - 09:51:22 CDT

The simplest would be to output a pdb file from the dcd file using catdcd
and then using that pdb file as a new starting point.

Purushottam

On Tue, Jul 28, 2015 at 10:45 AM, Daniela Rivas <dani.rivas.r_at_gmail.com>
wrote:

> 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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