Re: Interrupted Molecular Dynamics Simulation

From: Daniela Rivas (dani.rivas.r_at_gmail.com)
Date: Wed Jul 29 2015 - 10:25:29 CDT

Well, thanks to everyone who tried to help me. I started my simulation all
over again and now I made sure to generate the restart files. Now I won't
make the same mistake.

Thanks a lot :)
Daniela.

2015-07-28 12:34 GMT-03:00 Felipe Merino <felipe.merino_at_mpi-dortmund.mpg.de>
:

> Hi,
>
> On 28/07/15 16:51, Purushottam Dixit wrote:
>
> 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
>
> This won't work since you will randomize the velocities and it **won't**
> be a proper restart.
>
>
>
> 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
>>>>
>>>>
>>>
>>
>
> --
> 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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