From: Alex Balaeff (abalaeff_at_polarisqb.com)
Date: Sun Jul 12 2020 - 10:50:38 CDT
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> 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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