|
|
| Line 1: |
Line 1: |
| − | __NOTOC__
| + | dummy |
| − | 9ohdlY fw831f64td9glse934dkjga
| |
| − | | |
| − | == Description ==
| |
| − | | |
| − | This script is used to run replica exchange simulations. In most parallel
| |
| − | environments it will start the replica exchange server automatically. The
| |
| − | options <B>-n</B>, <B>-par</B>, <B>-temp</B>, <B>-condfile</B>, <B>-ens</B>,
| |
| − | <B>-ensdir</B> are available as in <docmark>rexserver.pl</docmark>.
| |
| − | Alternatively, it can connect to an external replica exchange server
| |
| − | if its address, port, and ID are given with <B>-rserv</B>. In that case
| |
| − | <B>-jobs</B> may be used to run only some of the temperature windows instead
| |
| − | of all windows if multiple clients are launched on different machines.<BR>
| |
| − | For shared memory environments the option <B>-cpus</B> can be used
| |
| − | to specify a smaller number of CPUs than temperature windows if necessary
| |
| − | due to computational restraints. A host file can be given with
| |
| − | <B>-hosts</B> for automatic remote submission in a distributed environment.
| |
| − | (see <docmark>calcprop.pl</docmark> for a more detailed explanation).<BR>
| |
| − | In order to contact the server from an external program (e.g. for monitoring
| |
| − | purposes) the server ID is required. The option
| |
| − | <B>-saveid</B> is available to write this server information to a file.
| |
| − | <BR>
| |
| − | The intial input PDB files for each MD simulation are expected either as
| |
| − | the last command line arguments or from an external file that is given with
| |
| − | <B>-f</B>.<BR>
| |
| − | The remaining parameters are used to control the MD simulations. Parameters
| |
| − | that can be given with <B>-mdpar</B> are shown <A HREF="http://mmtsb.scripps.edu/cgi-bin/charmmpar" TARGET=cpar>here</A>.<BR>
| |
| − | The option <B>-l</B> is available to provide a list of residues and
| |
| − | a template PDB structure for loop modeling. Please note that with this
| |
| − | option RMSD values that are automatically calculated if a reference PDB structure
| |
| − | is given are also limited to only these residues.<BR>
| |
| − | Further options given with
| |
| − | <B>-mdopt</B> control whether a trajectory or restart file is written out
| |
| − | (<font color=#508060>[no]trajout</font> and <font color=#508060>[no]restout</font>), how many MD steps
| |
| − | are used (default: 1) for averaging the energy score used in the replica exchange
| |
| − | Metropolis criteria (<font color=#508060>avgener</font>), whether the rest of protein is
| |
| − | restrained outside the loop (<font color=#508060>[no]conslim</font>), and the maximum
| |
| − | restraint force (<font color=#508060>limforce</font>) and type of restrained atoms (<font color=#508060>limsel</font>)
| |
| − | in this case. Other restraints may be specified with <B>-cons</B>.<BR>
| |
| − | The simulation protocol can be further customized by providing CHARMM commands
| |
| − | through external files. This can be done with <B>-custom</B> which expects a keyword
| |
| − | and a file name as arguments. The keyword is used to specify when the custom
| |
| − | command sequence should be inserted in the standard protocol. If <font color=#508060>setup</font>
| |
| − | is used the commands will be sent to CHARMM only once during the initial setup
| |
| − | phase. If the keywords <font color=#508060>pre</font> or <font color=#508060>post</font> the commands will
| |
| − | be executed before or after the dynamics command, respectively. These keywords
| |
| − | can be further qualified with <font color=#508060>:init</font>, <font color=#508060>:equi</font>, and <font color=#508060>:prod</font>
| |
| − | corresponding to the replica exchange cycle modes to allow custom equilibration
| |
| − | protocols.<BR>
| |
| − | The option <B>-log</B> is available to request a server log file. A CHARMM
| |
| − | log file is generated for each client if <B>-charmmlog</B> is given, an
| |
| − | energy log file is generated with <B>-elog</B>.
| |
| − | | |
| − | == Options ==
| |
| − | | |
| − | ; -help : usage information
| |
| − | | |
| − | | |
| − | == Examples ==
| |
| − | | |
| − | <mmtsbToolExample cmd="aarex.pl" set="/apps/mmtsb/bench/aarex.pl-test/test1"></mmtsbToolExample>
| |
| − | | |
| − | <mmtsbToolExample cmd="aarex.pl" set="/apps/mmtsb/bench/aarex.pl-test/test2"></mmtsbToolExample>
| |
| − | | |
| − | <mmtsbToolExample cmd="aarex.pl" set="/apps/mmtsb/bench/aarex.pl-test/test3"></mmtsbToolExample>
| |
| − | | |
| − | <mmtsbToolExample cmd="aarex.pl" set="/apps/mmtsb/bench/aarex.pl-test/test4"></mmtsbToolExample>
| |
| − | | |
| − | <mmtsbToolExample cmd="aarex.pl" set="/apps/mmtsb/bench/aarex.pl-test/test5"></mmtsbToolExample>
| |
| − | | |
| − | <mmtsbToolExample cmd="aarex.pl" set="/apps/mmtsb/bench/aarex.pl-test/test6"></mmtsbToolExample>
| |
| − | | |
| − | <mmtsbToolExample cmd="aarex.pl" set="/apps/mmtsb/bench/aarex.pl-test/test7"></mmtsbToolExample>
| |
| − | The condition file looks the following:
| |
| − | <pre>
| |
| − | bias rg
| |
| − | 298 force=1.25,target=18.0
| |
| − | 298 force=0.60,target=9.0
| |
| − | 298 force=0.60,target=13.0
| |
| − | 298 force=0.75,target=14.0
| |
| − | </pre>
| |
| − | | |
| − | <mmtsbToolExample cmd="aarex.pl" set="/apps/mmtsb/bench/aarex.pl-test/test8"></mmtsbToolExample>
| |
| − | with the following condition file:
| |
| − | <pre>
| |
| − | bias rg
| |
| − | 298 force=1.00,target=15.0
| |
| − | 298 force=0.60,target=12.0
| |
| − | 320 force=0.60,target=12.0
| |
| − | 320 force=1.00,target=15.0
| |
| − | </pre>
| |
| − | | |
| − | <mmtsbToolExample cmd="aarex.pl" set="/apps/mmtsb/bench/aarex.pl-test/test9"></mmtsbToolExample>
| |
