Re: Interrupted Molecular Dynamics Simulation

From: Felipe Merino (felipe.merino_at_mpi-dortmund.mpg.de)
Date: Tue Jul 28 2015 - 02:03:00 CDT

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
> <mailto: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 <mailto: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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