Folding a miniprotein, a starter protocol
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Input files
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- minip.top : topology file of protein T (Amber format)
- minip.crd : coordinates of atoms, extended, unfolded structure (Amber format)
- minip.pdb : PDB file plus charges and radii of atoms

Run minimization with sander. This is to remove any "hot spots" in 
the above structures. 
----------------------------
500 steps of steepest descent algorithm
500 steps of conjugate gradient algorithm
./sander_min.sh

Heating from 0k to 317k (experimentally known melting temperature of protein T)
-------------------
30ps of heating (from 0k to 317k)
20ps of md simulation at constant temperature T=317k
./cuda_equil.sh

Run 20ns of simulations
-----------------------
20ns if MD simulation at 317k (melting temperature)
it is possible to see folding unfolding events here
especially if we increase the simulation to 50ns or more. 
I recommend to run for about 1/2 day to collect several events. 

./cuda_equil.sh

Simulated Annealing
-------------------
Increase the temperature from 0k to 400k , 3ns
Then decrease temperature from 400k to 317k, 4ns
MD simulations at 317k , 2ns
./cuda_annealing.sh

Run 10ns of MD
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10ns of Molecular dynamics at 317k
You may want to do a longer simulation (50ns)



