I have run two indipendent jobs starting from the same input files except for the seed (ie setting option -jran 1234567 vs. -jran 1234568), in order to produce 1,000 loop models from each jobrun.
Each job is aimed to model simultaneously five loops of more than 14 residue length each one.
Once the jobruns has been accomplished I noticed that the two datasets of loop models generated from the jobs are almost the same (for instance, the model No 174 of job A is identical to the model No 185 of job B, and so on).
Could the absolute value/difference of the seeds influence on the mode by which the models are generated? If I set two seed as 1234567 and 7654321, will I obtain two really different dataset of loop models?
For more details...
I have adopted the next generation KIC protocol with fragments, using the following command line:
mpirun -np 128 loopmodel.mpi.linuxgccrelease -in:file:s template.pdb -extra_res_cen LG.cen.params -extra_res_fa LG.fa.params -loops:loop_file list.loop -loops:frag_sizes 9 3 1 -loops:frag_files 9mers 3mers none -constant_seed -jran 1234567 -nstruct 1000 @ flags
The initial template is a protein dimer complexed with a small molecule. The additional flags (flags file) are the following:
Thank you in advance