# surpass_annealing program¶

You need just a .ss2 file for your target protein to run the program. Provide it using -in:ss2 command line option. Other options are used to:

specify starting conformation

-model:random

starts the simulation from a random chain (extended conformation) while

-model:pdb

provides an input starting conformation

specify temperature set for simulated annealing run

-sample:t_start, -sample:t_end and -sample:t_steps define a set of N+1 temperatures distributed uniformly between the starting and the ending temperature
specify the length of the simulation (Monte Carlo steps)

-sample:mc_inner_cycles defines the amount of sampling between frames that are recorded sample:mc_cycle_factor makes every inner MC cycle longer (multiplying them by a given factor) -sample:mc_outer_cycles defines the number of frames recorded for every temperature value

The total number of MC steps is then $$N_{temperatures} \times N_{inner} \times N_{factor} \times N_{outer}$$

Example parameters for ab-initio simulation of a protein:

./surpass_annealing -model:random \
-in:ss2=test_inputs/2gb1A.ss2 \
-sample:t_start=2.2 \
-sample:t_end=0.9 \
-sample:t_steps=15 \
-sample:mc_outer_cycles=100 \
-sample:mc_inner_cycles=10 \
-sample:mc_cycle_factor=10 \


Example parameters to relax an input structure:

./surpass_annealing -model:pdb=2gb1A.pdb \
-in:ss2=test_inputs/2gb1A.ss2 \
-sample:t_start=2.2 \
-sample:t_end=0.9 \
-sample:t_steps=15 \
-sample:mc_outer_cycles=100 \
-sample:mc_inner_cycles=10 \
-sample:mc_cycle_factor=10 \