RE: Restarting aborted NAMD run

From: Raman Preet Singh (
Date: Wed Aug 12 2020 - 12:40:45 CDT

Hi Alexander,

Thank you very much for the detailed, step-by-step info. Really helpful.

Thanks again!

From: Alex Balaeff<>
Sent: 12 July 2020 21:20
To:<>; Raman Preet Singh<>
Subject: Re: namd-l: Restarting aborted NAMD run

Hi Raman:

Typically, you restart your simulation from the latest restart point saved before the crash. See the parameters restartname/restartfreq in the manual:

And you set the firsttimestep to that of that latest restart point. Then you will have to stitch together the DCD files.

For example, let's say that your original simulation:
- was aborted at step 12975000
- saved the latest DCD frame at the step 12974000 (dcdfreq=2000)
- and saved the latest restart point at the step 12950000 (restartfreq=50000)

Then you'll restart the simulation with firsttimestep=12950000 (remember to supply the correct file names - those of your saved restart point - to bincoordinates/binvelocities/extendedsystem). And you will end up with 2 dcds. One from steps 0-12974000, the other from steps 12950000-20000000 (presuming you run for 20 mln steps total). As you see, these DCDs have a 13-frame overlap: timesteps 12950000, 12952000, ..., 12974000. One removes those 13 frames from the first DCD and stitches the two DCDs together. You can use catdcd for that:



On Sun, Jul 12, 2020 at 4:57 AM Raman Preet Singh <<>> wrote:
Dear All,

I am a new NAMD user and have a very trivial question.

I ran a simulation which got aborted at step 12975000 (the last step in .xst file) due to power outage. Looking through the NAMD mailing list and NAMD tutorial, I believe that I need to restart my simulation with firsttimestep set to 12975000. Then I need to concatenate the two dcd files. Is this the correct way?


  Dr. Alexander Balaeff
  Polaris Quantum Biotech<>

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