From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Dec 24 2009 - 03:35:52 CST
Hello:
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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