Hello,
On Mon, Jan 18, 2010 at 9:13 AM, gunajyoti das <guna_das78.yahoo.co.in> wrote:
> Hi AMBER Users
>
> I am trying to carry out QMMM driven energy minimization on a double stranded RNA sequence having 5 nucleotides on each strands. I have added explicit water molecules as well as counterions too. I am treating all the RNA residues with QM using PM3 while the other parts are treated with classical MM.
>
> Now after doing even 199000 steps of steepest descent and 1000 steps of conjugate gradient minimization, the energy is still not stable. Kindly guide me how can I use the QMMM method to get a reliable optimized structure for my RNA sequence.
>
Steepest descent converges very slowly (in fact, it's not really a
convergent method at all). 199000 steps of steepest descent is a lot
of wasted computer effort. If you're trying to find a true minimum,
you'll probably want to switch to 1000 steps of steepest descent and
199000 steps of conjugate gradient, or (probably the better
suggestion), check out xmin and/or lmod and use one of those instead.
You can get descriptions of these in the amber manual. (check the
ntmin variable, as this controls the type of minimization routine that
is used)
Good luck!
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Jan 18 2010 - 08:30:03 PST
