latrex.pl

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Examples

latrex.pl -n 8 -par initruns=2,equilruns=2,seq=1vii.seq -temp 4:1.0:1.6
performs 8 cycles of replica exchange Monte Carlo lattice simulations with 2 initilization and 2 equilibration runs. The sequence file is required as input parameter and used to generate random input chains. 4 exponentially spaced temperature windows from 1 to 1.6 are used.

latrex.pl -n 8 -par initruns=2,equilruns=2,seq=1vii.seq -temp 4:1.0:1.6 -ens rex -ensdir data
runs replica exchange lattice simulations and stores the structures from the lowest temperature window in an ensemble.

latrex.pl -n 8 -par initruns=2,equilruns=2,seq=1vii.seq -temp 4:1.0:1.6 -input pdb 1vii.sample.?.pdb
runs a replica exchange lattice simulation starting from SICHO chains that have been generated from the given PDB input files rather than a random chain, generated by default.

latrex.pl -n 8 -par initruns=2,equilruns=2 -par seq=1vii.seq,rebuild,natpdb=1vii.exp.pdb -temp 4:1.0:1.6 -l 1vii.exp.pdb 10:21 -simopt limforce=2.0
runs replica exchange lattice simulations for a loop modeling application. The residues outside the loop are restrained during the simulation with a force of 2.0. The resulting chains are automatically rebuilt at each cycle and since the native structure is given, RMSD values between the reconstructed all-atom structure and the native structure are also calculated and stored.

latrex.pl -n 10 -par initruns=2,equilruns=2,seq=1vii.seq -temp 4:1.0:1.6 -hosts sgi.workstations
runs a distributed replica exchange lattice simulations. The host information is taken from sgi.workstations.

latrex.pl -n 10 -par initruns=2,equilruns=2,seq=1vii.seq -temp 4:1.0:1.6 -mp -hosts sgi.local
runs a distributed replica exchange lattice simulations with local directory. The host information is taken from sgi.local.