Warning: Not all atoms have unique coordinates

From: Jarrod Nickel (jarrod.nickel.17_at_gmail.com)
Date: Fri May 22 2009 - 14:08:34 CDT

I have a strange problem,
I am trying to equilibrate an 8 lipid membrane (4 lipids per leaflet)
solvated with water above and below. First I do a 100 step minimization,
then ask it to run for 500000 time steps (2fs timestep = 1ns total).
Everything runs just fine for the first 5100 time steps, then "Warning: Not
all atoms have unique coordinates" starts appearing in my .log file
repeatedly (approx. once every 10 time steps). This happens for a while (500
time steps) then the warning stops and the simulation carries on as normal
again (for about 600 time steps), then the warning reappears (for 900 time
steps) and eventually the simulation fails after 7100 time steps. The final
message given is "FATAL ERROR: Periodic cell has become too small for
original patch grid! Possible solutions are...."

I have read how to resolve the "periodic cell becoming too small" issue
(plus NAMD tells you how to resolve it) but my question is about the
repeated "atoms not having unique coordinates" warning. Are there any ideas
why my simulation can run for a period of time, produce a warning, run fine
again, then give a warning again and finally fail??? Why doesn't it fail the
first time the warning appears? How would I resolve this issue?

I see other people have had this "unique coordinate" issue, but generally it
occurs at the beginning of a simulation not part way through.

Any help and ideas would be greatly appreciated,

Jarrod

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