Hi Gunajyoti
> 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 is normally only good for moving away from high energies.
Ideally you want to do lots more conjugate gradient or ideally xmin (check
ntmin in the manual).
Note, what you are trying to minimize is a VERY large system. You are trying
to do minimization in explicit solvent and counterions. You have a HUGE
number of degrees of freedom here and really all you are doing is spending
most of your time trying to minimize the water. Plus you will only get a
local minimum. You should probably think about what you are trying to
achieve here. Why do you want a minimum? What do you hope to learn?
Optimizations in explicit water really won't tell you much, you will just
get minimized water.
All the best
Ross
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|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk |
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Received on Mon Jan 18 2010 - 22:00:02 PST
