Dear AMBER users,
While running NAMD simulations on DNA immersed in water, and using AMBER
forcefield (Cornell's 1994), I encountered the following problem:
During the first step of calculation (MD or minimization), the initial
box was split in 4 smaller boxes and displaced by about 3-4 A, plus the
structure was reflected in mirror planes along the main axes. The DNA
duplex was split into 2 individual chains and each of them displaced in
different positions. This problem is seen only when Periodic Boundary
Conditions are on.
I have performed numerous tests and trials and think this might be a bug
in NAMD code.
Any comments welcome
Grzegorz
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Received on Thu Aug 04 2005 - 19:53:00 PDT
