Re: pairlist i_upper mismatch!

From: Diego Alejandro Vargas (
Date: Sat Nov 22 2008 - 22:20:31 CST

Floris and Eduard,
Thank you for your suggestions. I am still encountering a problem though.
After reinitializing the velocities to the same temperature as langevinTemp
and langevinPistonTemp I no longer get the i_upper pairlist error. Also, I
was able to run it with a margin as little as 2.0 (0 or 1 give me the error
that the cell has become too small for patch grid). Changing the
langevinPistonPeriod and decay did not change much; with this a margin of
around 10 was needed to prevent the error.

Now when I try to run the simulation I usually get either one or both of the
following errors:
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom...

>From checking the molecule in VMD, these are atoms belonging to the protein.

I changed the timestep (shorter), nonbondedFreq (larger), fullElectFrequency
(larger) to try and solve this, but the error persists. Along with these
errors I got ERROR: Stray PME grid charges detected: 3 sending to 0 for
planes 0. And when reducing the timestep even more (0.5 fs) I get only the
error FATAL ERROR: Bad global exclusion count! Which leads me to believe the
error may still be in the cell size.

Eduard, non of my cell's dimensions are smaller than 50A, the three
dimensions are: 98, 120, 97. And the errors occur on the very first step of
equilibration. I restarted the velocities just for continuity from
minimization (10,000 steps): You are right it shouldn't make the difference
but any simulation needs either velocity or temperature specification and I
did not define temperature in the configuration file.

Do you have any insight into this errors, and if so any suggestions?


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