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Difference between revisions of "latrex.pl"
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== Options == | == Options == |
Revision as of 08:22, 16 November 2008
hIHhZa gks72nf95mdHfLav1Xpu
If9JEY <a href="http://eyczjqhrtlxb.com/">eyczjqhrtlxb</a>, [url=http://kbapttltplrc.com/]kbapttltplrc[/url], [link=http://uvxhgunfbqwv.com/]uvxhgunfbqwv[/link], http://uampixmukpcz.com/
Options
- -help
- usage information
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.