bilayer simulation keeps crashing

From: Chitrak Gupta (
Date: Tue Apr 14 2015 - 10:00:27 CDT

Dear NAMD users,

I am having trouble simulating an equilibrated bilayer. I generated the
POPS bilayer using charmm-gui website (, and equilibrated
the system using the scripts generated by the website itself.

After equilibration, the bilayer chains are not perfectly straight, but are
sticking out. I am trying to solvate it and run a simulation, but I am not
sure how to fix the PBC conditions. I have followed the steps from NAMD
membrane tutorial for solvating and setting up the PBC, but that gives the
following error:

ERROR: Constraint failure in RATTLE algorithm for atom

I have looked at the listed atoms, and it does seem like a chain from the
adjacent periodic box is overlapping with these atoms. However, if I make
the box dimension larger, I get the following error:

FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.

I have tried restarting from restart files as well as disabling the
flexible cell option, but the error has persisted. Does anyone know how to
solve this?


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