Hi,
One thing you might consider doing is adding a 'check' command with
the 'skipbadframes' option to skip over frames with corrupted
coordinates. In my experience when a NetCDF trajectory frame is
corrupted it tends to be an 'all or nothing' situation, so checking
the first few atoms of the system (for speed) usually suffices,
something like:
trajin <trajectory>
check .1-10 skipbadframes reportfile report.dat
trajout nobadframes.nc
Then check 'report.dat' for which frames had issues. I like doing this
as a first pass because if you have corrupted frames, things like
'autoimage' will fail anway. Hope this helps,
-Dan
On Wed, Jan 20, 2021 at 8:55 AM Ayesha Fatima <ayeshafatima.69.gmail.com> wrote:
>
> Dear all,
> Good evening
> Perhaps this question has been asked but I could not find what I was
> looking for, While running my production simulation, it crashed
> multiple times due to computer restarting for one reason or another. Now i
> want to combine them and i made the following input file
> ...........................................
> trajin 05-production1ns.nc 1 257900 1
> trajin 05-production1ns-1.nc 100 224900 1
> trajin 05-production1ns-2.nc 100 16800 1
> reference 04-eq-2.rst7
> autoimage
> center :1-60113 mass origin
> image origin center familiar
> trajout 05-production1ns-all.nc
>
> ............................................
> the command line I will run is ptraj -p complex_solv.prmtop <trajin.in>
> trajout.out
>
> Is this the correct way to run?
>
> Thank you
> Regards
> Ayesha
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Received on Fri Jan 22 2021 - 11:00:02 PST
