This command file for running a LINUS simulation will perform multiple simulations. Each simulation output will be in a new subdirectory; sim_1, sim_2, sim_3, etc. The user should edit the "range" to set the number simulations to be run. In the example below five simulations will be run.

    for i in range(5):

Make a copy of this file in your working directory and edit it appropriately. To run a LINUS simulation see the Examples section.

from pylinus_1_0 import linusSim, ran

def gen_seeds():
    from random import uniform
    s1 = long(uniform(1.0, ran.M1))
    s2 = long(uniform(1.0, ran.M1))
    s3 = long(uniform(1.0, ran.M1))
    s4 = long(uniform(1.0, ran.M2))
    s5 = long(uniform(1.0, ran.M2))
    s6 = long(uniform(1.0, ran.M2))
    return s1, s2, s3, s4, s5, s6

def run(file, seed=None):
    if seed is None:
        gen = apply(ran.generator, gen_seeds())
    else:
        gen = apply(ran.generator, seed)
        
    sim = linusSim.Linus(file, gen)
    
#Beginning of parameter section
    sim.set_simulation_parameters(numsave=100, 
                                  numcycle=5000)
    sim.set_hbond_parameters(use_hbond=1,
                             use_sidechain_hbond=1)
    sim.set_contact_parameters(use_contact=1)
#End of parameter section

    sim.run()

if __name__ == "__main__":
    try:
        import psyco
    except ImportError:
        pass
    else:
        psyco.bind(run)  
    import sys, os
    filename = sys.argv[1]
    basedir = os.getcwd()
    file = os.path.basename(filename)
    for i in range(5):
        curdir = basedir + os.sep + 'sim_' + `i+1`
        os.mkdir(curdir)
        os.link(filename, curdir+os.sep+file)
        os.chdir(curdir)
        run(file)