From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Wed Oct 14 2009 - 22:57:34 CDT
i simulated a protein system inserted in membrane in a water box with
ions (total charge is close to zero) with PBC. Box size 159x159x112 A.
NPT ensemble with electric field (of 1 namdconf unit) perpendicular to
membrane was applied. Simulation runs normally up to 1,000,000 steps
(2 ns) with normal decrease in total energy, temperature and pressures
correspond to target values. Only slight increase in water box (by a
couple of angstroms) was observed.
Then, during the following 1.4 ns the box size increases to
5190x5190x3650 A and visually everything explodes.
In other runs with exactly the same system but 10 times smaller
electric field 4.4 ns of simulations are as expected.
Should it explode when 10 ns is reached? Has anyone observed system
explosion _after_ the system is minimized and partially equilibrated?
-- Roman Petrenko Physics Department University of Cincinnati
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