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Sample LINUS Run Files

 

Minimal Run File

Multiple Simulation Run File

Read Weights Run File

Read Mesostate Run File

All Options Run File


LINUS

 

This command file will run a LINUS simulation with secondary structure conformation weights from a previous simulation instead of the default weights which are:


============================================================
 Conformation Weights 
============================================================
RESIDUE    HELIX   SHEET   TURN1   TURN2    COIL    PII
   1 ACE   0.000   0.000   0.000   0.000   1.000   0.000
   2 MET   0.000   0.000   0.000   0.000   1.000   0.000
   3 GLN   0.513   0.037   0.093   0.000   0.187   0.171
   4 ILE   0.544   0.042   0.050   0.048   0.156   0.161

The user should make a copy of the conformation weights file in the working directory.
(The conformation weights file would be an output file from a previous LINUS run and it has a name such as *_006_001.SWT):

cp [filename].SWT weights

Make a copy of the command file below in your working directory and edit it appropriately. To run a LINUS simulation with previous weights see the Example 3. section.


from pylinus_2_3 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,mlfile=None,wtsfile=None,msfile=None,
        pmsfile=None,distfile=None):
    if seed is None:
        gen = apply(ran.generator, gen_seeds())
    else:
        gen = apply(ran.generator, seed)
    sim = linusSim.Linus(file, gen)
    sim.load_movelist(mlfile)
    sim.set_simulation_parameters(numsave=100,
                                  numcycle=5000)
    sim.set_hbond_parameters(use_hbond=1)
    sim.set_contact_parameters(use_contact=1)
    sim.run()

if __name__ == "__main__":
    try:
        import psyco
    except ImportError:
        pass
    else:
        psyco.bind(run)  
    import sys, os
    filename = sys.argv[1]
    file = os.path.basename(filename)
    basedir = os.getcwd()

    wtsfile = os.path.abspath('weights')

#
# The loop below demonstrates how to launch multiple simulations
# from one command file.
# Increment the range to perform additional simulations
# 
# Note that the "weights" file needs to be linked in each sub-directory
#
    for i in range(5):       
        curdir = basedir + os.sep + 'sim_' + `i+1`
        os.mkdir(curdir)
        os.link(filename, curdir+os.sep+file)
        os.link('weights', curdir+os.sep+'weights')
        os.chdir(curdir)
        run(file,wtsfile=wtsfile)