RE: Restarting aborted NAMD run

From: Raman Preet Singh (ramanpreetsingh_at_hotmail.com)
Date: Wed Aug 12 2020 - 12:40:45 CDT

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Hi Alexander,

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

Thanks again!
RPS

From: Alex Balaeff<mailto:abalaeff_at_polarisqb.com>
Sent: 12 July 2020 21:20
To: namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>; Raman Preet Singh<mailto:ramanpreetsingh_at_hotmail.com>
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:
https://www.ks.uiuc.edu/Research/namd/2.14b2/ug/node12.html

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:

https://www.ks.uiuc.edu/Development/MDTools/catdcd/

Best,

Alexander.

On Sun, Jul 12, 2020 at 4:57 AM Raman Preet Singh <ramanpreetsingh_at_hotmail.com<mailto:ramanpreetsingh_at_hotmail.com>> 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?

Thanks,
Raman

--
 -----
  Dr. Alexander Balaeff
  Polaris Quantum Biotech
  www.PolarisQB.com<http://www.PolarisQB.com>
  (919)-270-5772

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