Re: Interrupted Molecular Dynamics Simulation

From: Chitrak Gupta (
Date: Mon Jul 27 2015 - 12:29:25 CDT

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,

On Mon, Jul 27, 2015 at 11:32 AM, Daniela Rivas <>

> 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.

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