> A nucleic acid (RNA) model in aqueous solution, using Ewald etc. was subjected
> to MD at 300K and nothing strange happened during the first 6 nanoseconds or
> so. Then, the mobility of the model started to slowly decrease which didn't
> draw my attention first, but after 11 ns, it was already very striking. At the
> end of the 20 ns run, the trajectory looked like during a heavily restrained
> MD - although no restraints were used after the initial equilibration 20 ns
> earlier. The output file showed energy and temperature parameters that didn't
> look strange at all - when you look at the entire trajectory it really looks
> like after a normal dynamics the model slowly stopped moving...
Take a look at a movie without doing any centering or imaging or RMS
fitting; what you will likely see is that the whole box is picking up
significant translational motion. I think what you are seeing is the
"flying block of ice" (see J. Comp. Chem. (2000) 21: 121-131 and J. Comp.
Chem. (1998) 19:726-740) where due to incomplete energy conservation and
temperature scaling, the kinetic energy of the low frequency modes (i.e.
translation) grows. In my experience, it is over that time scale. If you
have the block of ice, you should see thymine methyls spinning rapidly.
To avoid this, you must remove center of mass translation periodically
(NSCM=500). To get better energy conservation, use AMBER 8.0, make sure
the pairlist is heuristically updated (default), set the SHAKE tolerance
smaller than the default (TOL=0.0000001), and set the temperature/pressure
coupling times to be larger...
If you restrt from your last (at 20ns), setting NSCM=1 (and if using an
earlier version of sander, NTCM=1) will show you on the first step if
there was a significant drop in temperature as the translational motion
was removed. Based on what you are seeing, I would guess a temperature
drop in the 50-100K range.
If you are running with NSCM/NTCM turned on and you are seeing this
problem, please provide us with more details...
--tom
\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
-/-
/-\ tec3.utah.edu (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A
http://www.chpc.utah.edu/~cheatham
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Received on Thu Nov 24 2005 - 16:53:00 PST
