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 - 08:00:03 PST
