On Sun, Sep 01, 2013, sunyeping wrote:
>
> I am now trying do NAMD simulation of proteins with amber field
> field. The systems crash rapidly after several dozens of minimization
> steps. Three chains of the proteins break down apart and run out
> of the water box. The program stops just when the minimization and
> initiation of heating, and "ERROR: Constraint failure in RATTLE
> algorithm for atom......" appears. The discussion about RATTLE algorithm
> is very common on web, I have tried many suggestions put up in these
> disscusions, such as desceasing the timestep, increasing margin, and
> increasing the temperature gradurally during heating, but none of them
> works.
It's really the same advice for any program: if you have problems, run a
*short* simulation (say 10 steps), and print every step.
Depending on your protein, a "few dozen" minimizations steps may not be
enough. I don't know what all the "999999.99" values mean in NAMD, but you
could look in its manual.
You'd be likely to get more help on this list if you ran a few steps in one
of the amber programs, such as mdgx (if you have only AmberTools), or pmemd
(if you have Amber).
...dac
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Received on Sun Sep 01 2013 - 10:00:02 PDT
