Periodic cell has become too small

From: Francesco Pietra (
Date: Thu Dec 24 2009 - 03:35:52 CST


I have minimized a CG system of protein+bilayer+watersolvation with
protein+bilayer fixed

# Minimization
if {1} {
minimize 1000
reinitvels $temperature

run 25000

bringing it to 310K slowly:

# Gradual increase of temperature
if {1} {
reassignFreq 500
reassignTemp 10
reassignIncr 10
reassignHold 310

Then I tried to equilibrate the system, with same restraints, holding
the 310K temperature, disabling useFlexibleCell ad setting "margin 5".
After new 1000 steps of minimization, the run crashed with:

Periodic cell has become too small.

Any suggestion how to make the equilibration smoother (I guess that
there are too sudden changes) from users that came across a similar
problem would be welcome.

francesco pietra

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