Akshay,
The error message has important information that should help you in
understanding and resolving the issue.
You seem to be running an NPT simulation (?) and the volume of the
periodic box has changed significantly (therefore the density). Read the
message "The GPU code ..." carefully. So your choices are to run the
simulation on CPU (slower but more robust) or split your NPT run into
multiple runs with smaller number of steps (which may help or may not).
The next steps fail because they could not find the coordinate files --
perhaps they were expected restart coordinates from the failed simulation?
Pratul
Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)
Web: http://www.agarwal-lab.org/
On 12/18/2018 10:55 AM, Akshay Prabhakant wrote:
> I GOT THIS ERROR ON RUNNING AN EQUILIBRATING SCRIPT.
>
>
> equilibriation: started
> ERROR: Calculation halted. Periodic box dimensions have changed too much
> from their initial values.
> Your system density has likely changed by a large amount, probably from
> starting the simulation from a structure a long way from equilibrium.
>
> [Although this error can also occur if the simulation has blown up for
> some reason]
>
> The GPU code does not automatically reorganize grid cells and thus you
> will need to restart the calculation from the previous restart file.
> This will generate new grid cells and allow the calculation to continue.
> It may be necessary to repeat this restarting multiple times if your
> system
> is a long way from an equilibrated density.
>
> Alternatively you can run with the CPU code until the density has
> converged
> and then switch back to the GPU code.
>
> equilibriation: completed
> copy equilibriation mdcrd: started
> sending incremental file list
> cap_camp_dna.eq_02.nc
> 17,596,504 100% 125.94MB/s 0:00:00 (xfr#1, to-chk=0/1)
> copy equilibriation mdcrd: completed
> cp: cannot stat 'cap_camp_dna.eq_02.rst': No such file or directory
> production run #1: started at Sun Dec 16 10:55:14 IST 2018
> STOP PMEMD Terminated Abnormally!
>
> Unit 9 Error on OPEN: cap_camp_dna.prod_0.rst
>
>
>
> production run #1: completed at Sun Dec 16 10:55:15 IST 2018
> copy production run #1 mdcrd: started
> sending incremental file list
> rsync: link_stat "/scratch/akpmnmy2j/md_cap_camp_dna_100ns/
> cap_camp_dna.prod_1.nc" failed: No such file or directory (2)
> rsync error: some files/attrs were not transferred (see previous errors)
> (code 23) at main.c(1183) [sender=3.1.1]
> copy production run #1 mdcrd: completed
> production run #2: started at Sun Dec 16 10:55:16 IST 2018
> STOP PMEMD Terminated Abnormally!
>
> Unit 9 Error on OPEN: cap_camp_dna.prod_1.rst
>
>
>
> production run #2: completed at Sun Dec 16 10:55:17 IST 2018
> copy production run #2 mdcrd: started
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Received on Tue Dec 18 2018 - 08:30:02 PST
