Difference between revisions of "latrex.pl"

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.

@@ Line 2: / Line 2: @@
 hIHhZa gks72nf95mdHfLav1Xpu
-== Description ==
+If9JEY  <a href="http://eyczjqhrtlxb.com/">eyczjqhrtlxb</a>, [url=http://kbapttltplrc.com/]kbapttltplrc[/url], [link=http://uvxhgunfbqwv.com/]uvxhgunfbqwv[/link], http://uampixmukpcz.com/
-This script is used to run replica exchange lattice Monte Carlo simulations
-with MONSSTER. Most of the options are identical to the options in
-<docmark>aarex.pl</docmark>. This script will also start up a server automatically
-in most parallel environment or can connect to a server that has been
-started manually with <docmark>rexserver.pl</docmark><font color=#508060> -monsster</font>.<BR>
-Input files may be given as in <docmark>aarex.pl</docmark> but can be either
-in PDB or SICHO chain format. The format has to be specified with <B>-input</B>.
-If no input files are given, random initial conformations are generated.<BR>
-Lattice simulations require a sequence file that needs to be identified by using
-the <font color=#508060>seq</font> parameter in the <B>-par</B> option. The parameter
-<font color=#508060>rebuild</font> also only applies to lattice simulations and controls whether
-the final lattice chains is automatically rebuild to an all-atom model. Depending
-on the length of each Monte Carlo cycle this may slow down the overall simulation
-time quite significantly since it is done by the server in a serial fashion.<BR>
-Lattice simulation specific parameters are set with <B>-simpar</B>
-(see <docmark>latticesim.pl</docmark> for a detailed explanation). The lattice
-grid size and restraint force constant for loop modeling may be given
-with <B>-simopt</B>. Finally, as in <docmark>latticesim.pl</docmark>
-distance restraints to be applied during the simulations can be given with
-<B>-d</B>.
 == Options ==