Re: Interrupted Molecular Dynamics Simulation

From: Daniela Rivas (
Date: Mon Jul 27 2015 - 19:21:00 CDT

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 :(


2015-07-27 14:29 GMT-03:00 Chitrak Gupta <>:

> 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 <>
> 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.

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