AMBER Archive (2006)

Subject: AMBER: MMPBSA: positive energies during nmode

From: Zu Thur Yew (yewzt_at_intern.bii-sg.org)
Date: Wed Aug 16 2006 - 09:15:11 CDT

Hi,

I tried to do nmode via the MMPBSA scripts with my system of 561
residues, but the energy's +ve after 3000 steps (4 x 10^2). The snapshot
used was extracted after 100ps of equilibration. My colleague has
noticed something similar with snapshots extracted across a 10ns MD run.
Amber was re-compiled to accommodate the large system size.

Looking at the minimizations done before MD runs, the energy drops to
-ve values within 500 steps or so and the MM energies for the snapshot
is -ve as well. Is this normal behavior & the energy will drop if I use
a large number of steps (say millions)? or am I missing something? Is it
something wrong with the recompiled Amber?

Any help/advice would be very much appreciated.

Thanks!

ZT
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