[Swift-commit] r5871 - in SwiftApps/CMTS: . rmsd rmsd/conf rmsd/docs rmsd/docs/images rmsd/docs/images/icons rmsd/docs/stylesheets rmsd/input_files
davidk at ci.uchicago.edu
davidk at ci.uchicago.edu
Thu Jul 26 15:47:08 CDT 2012
Author: davidk
Date: 2012-07-26 15:47:04 -0500 (Thu, 26 Jul 2012)
New Revision: 5871
Added:
SwiftApps/CMTS/rmsd/
SwiftApps/CMTS/rmsd/README
SwiftApps/CMTS/rmsd/TODO
SwiftApps/CMTS/rmsd/conf/
SwiftApps/CMTS/rmsd/conf/beagle.cf
SwiftApps/CMTS/rmsd/conf/beagle.xml
SwiftApps/CMTS/rmsd/conf/grotthuss.cf
SwiftApps/CMTS/rmsd/conf/grotthuss.xml
SwiftApps/CMTS/rmsd/conf/local.cf
SwiftApps/CMTS/rmsd/conf/local.xml
SwiftApps/CMTS/rmsd/conf/makena.cf
SwiftApps/CMTS/rmsd/conf/makena.xml
SwiftApps/CMTS/rmsd/conf/mcs.cf
SwiftApps/CMTS/rmsd/conf/mcs.conf
SwiftApps/CMTS/rmsd/conf/pads.cf
SwiftApps/CMTS/rmsd/conf/pads.xml
SwiftApps/CMTS/rmsd/docs/
SwiftApps/CMTS/rmsd/docs/README
SwiftApps/CMTS/rmsd/docs/build_docs.sh
SwiftApps/CMTS/rmsd/docs/images/
SwiftApps/CMTS/rmsd/docs/images/icons/
SwiftApps/CMTS/rmsd/docs/images/icons/caution.png
SwiftApps/CMTS/rmsd/docs/images/icons/example.png
SwiftApps/CMTS/rmsd/docs/images/icons/home.png
SwiftApps/CMTS/rmsd/docs/images/icons/important.png
SwiftApps/CMTS/rmsd/docs/images/icons/next.png
SwiftApps/CMTS/rmsd/docs/images/icons/note.png
SwiftApps/CMTS/rmsd/docs/images/icons/prev.png
SwiftApps/CMTS/rmsd/docs/images/icons/tip.png
SwiftApps/CMTS/rmsd/docs/images/icons/up.png
SwiftApps/CMTS/rmsd/docs/images/icons/warning.png
SwiftApps/CMTS/rmsd/docs/stylesheets/
SwiftApps/CMTS/rmsd/docs/stylesheets/asciidoc.css
SwiftApps/CMTS/rmsd/input_files/
SwiftApps/CMTS/rmsd/input_files/cg_clath_cage.conf
SwiftApps/CMTS/rmsd/input_files/cg_clath_cage.pdb
SwiftApps/CMTS/rmsd/input_files/cg_clath_cage.psf
SwiftApps/CMTS/rmsd/input_files/par_cg_clath.inp
SwiftApps/CMTS/rmsd/input_files/rmsd.temp.tcl
SwiftApps/CMTS/rmsd/rmsd.sh
SwiftApps/CMTS/rmsd/rmsd.swift
SwiftApps/CMTS/rmsd/runrmsd.sh
Log:
Adding rmsd scripts
Added: SwiftApps/CMTS/rmsd/README
===================================================================
--- SwiftApps/CMTS/rmsd/README (rev 0)
+++ SwiftApps/CMTS/rmsd/README 2012-07-26 20:47:04 UTC (rev 5871)
@@ -0,0 +1,74 @@
+CMTS rmsd Swift Scripts
+=======================
+
+Prerequisites
+-------------
+This README will assume that runs will be started from
+makena.uchicago.edu.
+
+Please ensure that namd2, vmd, and Swift are in your $PATH. These
+applications must be available from the Makena worker
+nodes (applications kept in /state do not seem to be
+available by the worker nodes).
+
+Add the following line to $HOME/.bashrc to set the PATH:
+-----
+export PATH=/scratch/davidk/swift-trunk/cog/modules/swift/dist/swift-svn/bin:/Network/Servers/vothfile.uchicago.edu/home/davidk/namd_2.8-intel-openmpi:/Network/Servers/vothfile.uchicago.edu/home/davidk/namd_2.8-intel-openmpi/vmd-1.9/bin:$PATH
+-----
+
+You will need to create a directory called /scratch/<yourusername>:
+-----
+mkdir /scratch/yourusername
+cd /scratch/yourusername
+-----
+
+IMPORTANT: Please note that runs may fail if started from /home due to some
+potential NFS issues, so please make sure to always use /scratch.
+
+
+Checking out scripts from SVN
+-----------------------------
+From within your scratch directory, run the following command to get a
+rmsd scripts:
+
+-----
+svn checkout https://svn.ci.uchicago.edu/svn/cmts/app/trunk/rmsd
+-----
+
+These scripts can periodically be updated by running an SVN update within
+the rmsd directory:
+-----
+svn update
+-----
+
+How to Run
+----------
+The runrmsd.sh script is used to start a run. The options you pass to
+this script will determine how the rmsd script runs.
+
+Usage: runrmsd.sh [-s sitename]
+
+The sitename option determines where a run will take place. Currently, the
+only tested option is "makena".
+
+Example:
+
+-----
+./runrmsd.sh -s makena
+-----
+
+When your job has finished running for the first time, you will see that a directory
+has been created called run001. A new directory will be created each time you run
+the runrmsd.sh script.
+
+Outputs
+-------
+Within each run<NNN> directory is a subdirectory called output. This directory will
+contain all relevent outputs created during the run. Currently this is the DCD file
+generated by namd.
+
+Logs
+----
+Within each run<NNN> directory is a subdirectory called logs. This directory contains
+the standard output and standard error logs from each namd task. If you notice a job
+is failing, reference these files for more detail about what went wrong.
Added: SwiftApps/CMTS/rmsd/TODO
===================================================================
--- SwiftApps/CMTS/rmsd/TODO (rev 0)
+++ SwiftApps/CMTS/rmsd/TODO 2012-07-26 20:47:04 UTC (rev 5871)
@@ -0,0 +1,5 @@
+Run on Makena, Grothis, Beagle, PADS
+Data management
+Turn swiftopt into a general swiftrun
+Clean up sed stuff
+
Added: SwiftApps/CMTS/rmsd/conf/beagle.cf
===================================================================
--- SwiftApps/CMTS/rmsd/conf/beagle.cf (rev 0)
+++ SwiftApps/CMTS/rmsd/conf/beagle.cf 2012-07-26 20:47:04 UTC (rev 5871)
@@ -0,0 +1,10 @@
+wrapperlog.always.transfer=true
+sitedir.keep=true
+execution.retries=3
+lazy.errors=true
+status.mode=provider
+use.provider.staging=false
+provider.staging.pin.swiftfiles=false
+
+#app sumloss=$PWD/../sumloss.sh
+#app evolve=$PWD/../evolve.sh
Added: SwiftApps/CMTS/rmsd/conf/beagle.xml
===================================================================
--- SwiftApps/CMTS/rmsd/conf/beagle.xml (rev 0)
+++ SwiftApps/CMTS/rmsd/conf/beagle.xml 2012-07-26 20:47:04 UTC (rev 5871)
@@ -0,0 +1,23 @@
+<config>
+ <pool handle="beagle">
+ <execution provider="coaster" jobmanager="local:pbs"/>
+
+ <profile namespace="env" key="SWIFT_GEN_SCRIPTS">KEEP</profile>
+
+ <profile namespace="globus" key="jobsPerNode">1</profile>
+ <profile namespace="globus" key="lowOverAllocation">100</profile>
+ <profile namespace="globus" key="highOverAllocation">100</profile>
+ <profile namespace="globus" key="providerAttributes">pbs.aprun;pbs.mpp;depth=24</profile>
+ <profile namespace="globus" key="maxTime">10000</profile>
+ <profile namespace="globus" key="maxWallTime">01:30:00</profile>
+ <profile namespace="globus" key="slots">50</profile>
+ <profile namespace="globus" key="nodeGranularity">2</profile>
+ <profile namespace="globus" key="maxNodes">2</profile>
+ <profile namespace="globus" key="queue">route</profile>
+ <profile namespace="karajan" key="jobThrottle">9.59</profile>
+ <profile namespace="karajan" key="initialScore">10000</profile>
+ <filesystem provider="local"/>
+ <workdirectory>_WORK_/beagle</workdirectory>
+ </pool>
+</config>
+
Added: SwiftApps/CMTS/rmsd/conf/grotthuss.cf
===================================================================
--- SwiftApps/CMTS/rmsd/conf/grotthuss.cf (rev 0)
+++ SwiftApps/CMTS/rmsd/conf/grotthuss.cf 2012-07-26 20:47:04 UTC (rev 5871)
@@ -0,0 +1,10 @@
+wrapperlog.always.transfer=true
+sitedir.keep=true
+execution.retries=0
+lazy.errors=true
+status.mode=provider
+use.provider.staging=false
+provider.staging.pin.swiftfiles=false
+use.wrapper.staging=false
+
+#app rmsd=$PWD/../rmsd.sh
Added: SwiftApps/CMTS/rmsd/conf/grotthuss.xml
===================================================================
--- SwiftApps/CMTS/rmsd/conf/grotthuss.xml (rev 0)
+++ SwiftApps/CMTS/rmsd/conf/grotthuss.xml 2012-07-26 20:47:04 UTC (rev 5871)
@@ -0,0 +1,19 @@
+<config>
+<pool handle="grotthuss">
+ <execution jobmanager="local:pbs" provider="pbs" url="none"/>
+ <filesystem provider="local" url="none" />
+ <profile namespace="globus" key="maxWallTime">01:00:00</profile>
+ <profile namespace="globus" key="maxTime">3600</profile>
+ <profile key="jobsPerNode" namespace="globus">8</profile>
+ <profile key="slots" namespace="globus">1</profile>
+ <profile key="maxNodes" namespace="globus">1</profile>
+ <profile key="queue" namespace="globus">devel</profile>
+ <profile key="jobThrottle" namespace="karajan">5.99</profile>
+ <profile key="initialScore" namespace="karajan">10000</profile>
+ <profile key="count" namespace="globus">1</profile>
+ <profile key="jobType" namespace="globus">single</profile>
+ <profile key="ppn" namespace="globus">8</profile>
+ <workdirectory>_WORK_</workdirectory>
+</pool>
+</config>
+
Added: SwiftApps/CMTS/rmsd/conf/local.cf
===================================================================
--- SwiftApps/CMTS/rmsd/conf/local.cf (rev 0)
+++ SwiftApps/CMTS/rmsd/conf/local.cf 2012-07-26 20:47:04 UTC (rev 5871)
@@ -0,0 +1,10 @@
+wrapperlog.always.transfer=true
+sitedir.keep=true
+execution.retries=0
+lazy.errors=true
+status.mode=provider
+use.provider.staging=false
+provider.staging.pin.swiftfiles=false
+use.wrapper.staging=false
+
+#app rmsd=$PWD/../rmsd.sh
Added: SwiftApps/CMTS/rmsd/conf/local.xml
===================================================================
--- SwiftApps/CMTS/rmsd/conf/local.xml (rev 0)
+++ SwiftApps/CMTS/rmsd/conf/local.xml 2012-07-26 20:47:04 UTC (rev 5871)
@@ -0,0 +1,14 @@
+<config>
+ <pool handle="localhost">
+ <filesystem provider="local" />
+ <execution provider="coaster" jobmanager="local:local"/>
+ <profile namespace="karajan" key="jobthrottle">2.55</profile>
+ <profile namespace="karajan" key="initialScore">10000</profile>
+ <profile namespace="globus" key="jobsPerNode">4</profile>
+ <profile namespace="globus" key="slots">8</profile>
+ <profile namespace="globus" key="maxTime">1000</profile>
+ <profile namespace="globus" key="nodeGranularity">1</profile>
+ <profile namespace="globus" key="maxNodes">4</profile>
+ <workdirectory>/tmp</workdirectory>
+ </pool>
+</config>
Added: SwiftApps/CMTS/rmsd/conf/makena.cf
===================================================================
--- SwiftApps/CMTS/rmsd/conf/makena.cf (rev 0)
+++ SwiftApps/CMTS/rmsd/conf/makena.cf 2012-07-26 20:47:04 UTC (rev 5871)
@@ -0,0 +1,10 @@
+wrapperlog.always.transfer=true
+sitedir.keep=true
+execution.retries=0
+lazy.errors=true
+status.mode=provider
+use.provider.staging=false
+provider.staging.pin.swiftfiles=false
+use.wrapper.staging=false
+
+#app rmsd=$PWD/../rmsd.sh
Added: SwiftApps/CMTS/rmsd/conf/makena.xml
===================================================================
--- SwiftApps/CMTS/rmsd/conf/makena.xml (rev 0)
+++ SwiftApps/CMTS/rmsd/conf/makena.xml 2012-07-26 20:47:04 UTC (rev 5871)
@@ -0,0 +1,20 @@
+<config>
+<pool handle="makena">
+ <execution jobmanager="local:pbs" provider="pbs" url="none"/>
+ <filesystem provider="local" url="none" />
+ <profile namespace="globus" key="maxWallTime">01:00:00</profile>
+ <profile namespace="globus" key="maxTime">3600</profile>
+ <profile key="jobsPerNode" namespace="globus">8</profile>
+ <profile key="slots" namespace="globus">1</profile>
+ <profile key="nodeGranularity" namespace="globus">2</profile>
+ <profile key="maxNodes" namespace="globus">2</profile>
+ <profile key="queue" namespace="globus">devel</profile>
+ <profile key="jobThrottle" namespace="karajan">5.99</profile>
+ <profile key="initialScore" namespace="karajan">10000</profile>
+ <profile key="count" namespace="globus">2</profile>
+ <profile key="jobType" namespace="globus">single</profile>
+ <profile key="ppn" namespace="globus">8</profile>
+ <workdirectory>_WORK_</workdirectory>
+</pool>
+</config>
+
Added: SwiftApps/CMTS/rmsd/conf/mcs.cf
===================================================================
--- SwiftApps/CMTS/rmsd/conf/mcs.cf (rev 0)
+++ SwiftApps/CMTS/rmsd/conf/mcs.cf 2012-07-26 20:47:04 UTC (rev 5871)
@@ -0,0 +1,7 @@
+wrapperlog.always.transfer=true
+sitedir.keep=true
+execution.retries=3
+lazy.errors=true
+status.mode=provider
+use.provider.staging=false
+provider.staging.pin.swiftfiles=false
Added: SwiftApps/CMTS/rmsd/conf/mcs.conf
===================================================================
--- SwiftApps/CMTS/rmsd/conf/mcs.conf (rev 0)
+++ SwiftApps/CMTS/rmsd/conf/mcs.conf 2012-07-26 20:47:04 UTC (rev 5871)
@@ -0,0 +1,45 @@
+# Keep all interesting settings in one place
+# User should modify this to fit environment
+
+# Location of SWIFT. If empty, PATH is referenced
+export SWIFT=
+
+# Where to place/launch worker.pl on the remote machine for sites.xml
+export WORKER_LOCATION=_RUNDIR_
+
+# How to launch workers: local, ssh, or cobalt
+export WORKER_MODE=ssh
+
+# Worker logging setting passed to worker.pl for sites.xml
+export WORKER_LOGGING_LEVEL=INFO
+
+# User name to use for all systems
+export WORKER_USERNAME=$USER
+
+# Worker host names for ssh
+export WORKER_HOSTS="crush thwomp stomp crank steamroller grind churn trounce thrash vanquish"
+
+# Directory to keep log files, relative to working directory when launching start-coaster-service
+export LOG_DIR=logs
+export WORKER_LOG_DIR=_RUNDIR_
+
+# Manually define ports. If not specified, ports will be automatically generated
+export LOCAL_PORT=
+export SERVICE_PORT=
+
+# Set shared filesystem to no since work will be done in local /sandbox directory
+export SHARED_FILESYSTEM=yes
+
+# start-coaster-service tries to automatically detect IP address.
+# Specify here if auto detection is not working correctly
+export IPADDR=
+
+# Below are various settings to give information about how to create sites.xml
+#export WORK=_RUNDIR_
+export JOBS_PER_NODE=1
+# export JOB_THROTTLE=$( echo "scale=5; $( echo $WORKER_HOSTS | wc -w )/100 - 0.00001"|bc )
+
+# Swift applications
+#app sumloss=$PWD/../sumloss.sh
+#app evolve=$PWD/../evolve.sh
+
Added: SwiftApps/CMTS/rmsd/conf/pads.cf
===================================================================
--- SwiftApps/CMTS/rmsd/conf/pads.cf (rev 0)
+++ SwiftApps/CMTS/rmsd/conf/pads.cf 2012-07-26 20:47:04 UTC (rev 5871)
@@ -0,0 +1,10 @@
+wrapperlog.always.transfer=true
+sitedir.keep=true
+execution.retries=3
+lazy.errors=true
+status.mode=provider
+use.provider.staging=false
+provider.staging.pin.swiftfiles=false
+
+#app sumloss=$PWD/../sumloss.sh
+#app evolve=$PWD/../evolve.sh
Added: SwiftApps/CMTS/rmsd/conf/pads.xml
===================================================================
--- SwiftApps/CMTS/rmsd/conf/pads.xml (rev 0)
+++ SwiftApps/CMTS/rmsd/conf/pads.xml 2012-07-26 20:47:04 UTC (rev 5871)
@@ -0,0 +1,30 @@
+<config>
+ <pool handle="local" >
+ <execution provider="local" url="none" />
+ <profile namespace="karajan" key="jobThrottle">0.09</profile>
+ <profile namespace="karajan" key="initialScore">10000</profile>
+ <filesystem provider="local"/>
+ <workdirectory>_WORK_/local</workdirectory>
+ </pool>
+ <pool handle="pads">
+ <execution provider="coaster" jobmanager="local:pbs" />
+ <filesystem provider="local"/>
+ <workdirectory>_WORK_/pads</workdirectory>
+
+ <profile namespace="globus" key="ppn">8</profile>
+ <profile namespace="globus" key="jobsPerNode">1</profile>
+ <profile namespace="globus" key="lowOverAllocation">100</profile>
+ <profile namespace="globus" key="highOverAllocation">100</profile>
+ <profile namespace="globus" key="maxTime">3600</profile>
+ <profile namespace="globus" key="maxWallTime">00:02:00</profile>
+ <profile namespace="globus" key="slots">192</profile>
+ <profile namespace="globus" key="nodeGranularity">1</profile>
+ <profile namespace="globus" key="maxNodes">1</profile>
+ <profile namespace="globus" key="queue">fast</profile>
+
+ <profile namespace="karajan" key="jobThrottle">0.5</profile>
+ <profile namespace="karajan" key="initialScore">10000</profile>
+
+ <profile namespace="env" key="SWIFT_GEN_SCRIPTS">KEEP</profile>
+ </pool>
+</config>
Added: SwiftApps/CMTS/rmsd/docs/README
===================================================================
--- SwiftApps/CMTS/rmsd/docs/README (rev 0)
+++ SwiftApps/CMTS/rmsd/docs/README 2012-07-26 20:47:04 UTC (rev 5871)
@@ -0,0 +1 @@
+link ../README
\ No newline at end of file
Property changes on: SwiftApps/CMTS/rmsd/docs/README
___________________________________________________________________
Added: svn:special
+ *
Added: SwiftApps/CMTS/rmsd/docs/build_docs.sh
===================================================================
--- SwiftApps/CMTS/rmsd/docs/build_docs.sh (rev 0)
+++ SwiftApps/CMTS/rmsd/docs/build_docs.sh 2012-07-26 20:47:04 UTC (rev 5871)
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+echo Converting $directory"$file" to HTML
+ asciidoc -a toc -a toclevels=2 \
+ -a max-width=750px \
+ -a textwidth=80 \
+ -a stylesheet=$PWD/stylesheets/asciidoc.css \
+ README
+
+echo Converting $directory"$file" to PDF
+ a2x --format=pdf --no-xmllint README
Property changes on: SwiftApps/CMTS/rmsd/docs/build_docs.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftApps/CMTS/rmsd/docs/images/icons/caution.png
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+ application/octet-stream
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+ application/octet-stream
Added: SwiftApps/CMTS/rmsd/docs/stylesheets/asciidoc.css
===================================================================
--- SwiftApps/CMTS/rmsd/docs/stylesheets/asciidoc.css (rev 0)
+++ SwiftApps/CMTS/rmsd/docs/stylesheets/asciidoc.css 2012-07-26 20:47:04 UTC (rev 5871)
@@ -0,0 +1,2 @@
+a:link { color:navy; }
+a:visited { color:navy; }
Added: SwiftApps/CMTS/rmsd/input_files/cg_clath_cage.conf
===================================================================
--- SwiftApps/CMTS/rmsd/input_files/cg_clath_cage.conf (rev 0)
+++ SwiftApps/CMTS/rmsd/input_files/cg_clath_cage.conf 2012-07-26 20:47:04 UTC (rev 5871)
@@ -0,0 +1,83 @@
+# NAMD Config file - autogenerated by NAMDgui plugin
+# Author: Jan Saam, saam at charite.de
+
+# input
+coordinates cg_clath_cage.pdb
+structure cg_clath_cage.psf
+parameters par_cg_clath.inp
+paratypecharmm on
+
+# output
+set output output/cg_clath_cage
+outputname $output
+dcdfile ${output}.dcd
+xstFile ${output}.xst
+dcdfreq 1000
+xstFreq 1000
+
+binaryoutput yes
+binaryrestart yes
+outputEnergies 1000
+restartfreq 1000
+
+fixedAtoms off
+
+# Basic dynamics
+exclude scaled1-4
+1-4scaling 1
+COMmotion no
+dielectric 1.0
+
+
+# Simulation space partitioning
+cutoff 350
+switching on
+switchdist 348
+pairlistdist 352
+
+# Multiple timestepping
+firsttimestep 0
+timestep 10
+stepspercycle 1
+nonbondedFreq 1
+fullElectFrequency 1
+rigidBonds all
+
+# Temperature control
+
+set temperature 310
+temperature $temperature; # initial temperature
+
+# Langevin Dynamics
+langevin on; # do langevin dynamics
+langevinDamping 0.001 # damping coefficient (gamma) of 1/ps
+langevinTemp $temperature; # bath temperature
+langevinHydrogen no; # don't couple langevin bath to hydrogens
+
+
+
+# Scripting
+
+# Simulated Annealing
+#reassignFreq 10000
+#reassignTemp 310
+#minimize 10000
+#for { set TEMP 310 } { $TEMP <= 650 } { incr TEMP 5 } {
+# run 10000
+# reassignTemp $TEMP
+# langevinTemp $TEMP
+#}
+#
+#run 1000000
+#
+#for { set TEMP 650 } { $TEMP >= 310 } { incr TEMP -5 } {
+# reassignTemp $TEMP
+# langevinTemp $TEMP
+# run 10000
+#}
+#run 1000000
+
+minimize 1000
+reinitvels $temperature
+run 2000
+
Property changes on: SwiftApps/CMTS/rmsd/input_files/cg_clath_cage.conf
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftApps/CMTS/rmsd/input_files/cg_clath_cage.pdb
===================================================================
--- SwiftApps/CMTS/rmsd/input_files/cg_clath_cage.pdb (rev 0)
+++ SwiftApps/CMTS/rmsd/input_files/cg_clath_cage.pdb 2012-07-26 20:47:04 UTC (rev 5871)
@@ -0,0 +1,470 @@
+REMARK original generated coordinate pdb file
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Property changes on: SwiftApps/CMTS/rmsd/input_files/cg_clath_cage.pdb
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftApps/CMTS/rmsd/input_files/cg_clath_cage.psf
===================================================================
--- SwiftApps/CMTS/rmsd/input_files/cg_clath_cage.psf (rev 0)
+++ SwiftApps/CMTS/rmsd/input_files/cg_clath_cage.psf 2012-07-26 20:47:04 UTC (rev 5871)
@@ -0,0 +1,1078 @@
+PSF
+
+ 38 !NTITLE
+ REMARKS original generated structure x-plor psf file
+ REMARKS topology top_cg_clath.impr.inp
+ REMARKS segment A0 { first NONE; last NONE; auto angles }
+ REMARKS segment B0 { first NONE; last NONE; auto angles }
+ REMARKS segment C0 { first NONE; last NONE; auto angles }
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+ REMARKS segment B1 { first NONE; last NONE; auto angles }
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+ REMARKS segment A2 { first NONE; last NONE; auto angles }
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+ REMARKS segment C2 { first NONE; last NONE; auto angles }
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+ REMARKS segment C3 { first NONE; last NONE; auto angles }
+ REMARKS segment A4 { first NONE; last NONE; auto angles }
+ REMARKS segment B4 { first NONE; last NONE; auto angles }
+ REMARKS segment C4 { first NONE; last NONE; auto angles }
+ REMARKS segment A5 { first NONE; last NONE; auto angles }
+ REMARKS segment B5 { first NONE; last NONE; auto angles }
+ REMARKS segment C5 { first NONE; last NONE; auto angles }
+ REMARKS segment A6 { first NONE; last NONE; auto angles }
+ REMARKS segment B6 { first NONE; last NONE; auto angles }
+ REMARKS segment C6 { first NONE; last NONE; auto angles }
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+ REMARKS segment C7 { first NONE; last NONE; auto angles }
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+ REMARKS segment B8 { first NONE; last NONE; auto angles }
+ REMARKS segment C8 { first NONE; last NONE; auto angles }
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+ REMARKS segment C9 { first NONE; last NONE; auto angles }
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+ REMARKS segment B10 { first NONE; last NONE; auto angles }
+ REMARKS segment C10 { first NONE; last NONE; auto angles }
+ REMARKS segment A11 { first NONE; last NONE; auto angles }
+ REMARKS segment B11 { first NONE; last NONE; auto angles }
+ REMARKS segment C11 { first NONE; last NONE; auto angles }
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+ 467 C11 1 CLA AK3 AK 0.000000 34620.7800 0
+ 468 C11 1 CLA LT3 LT 0.000000 55013.7800 0
+
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+
+ 0 !NPHI: dihedrals
+
+
+ 468 !NIMPHI: impropers
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+
+ 0 !NDON: donors
+
+
+ 0 !NACC: acceptors
+
+
+ 0 !NNB
+
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+ 0 0 0 0 0 0 0 0
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+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0
+
+ 1 0 !NGRP
+ 0 0 0
+
Property changes on: SwiftApps/CMTS/rmsd/input_files/cg_clath_cage.psf
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftApps/CMTS/rmsd/input_files/par_cg_clath.inp
===================================================================
--- SwiftApps/CMTS/rmsd/input_files/par_cg_clath.inp (rev 0)
+++ SwiftApps/CMTS/rmsd/input_files/par_cg_clath.inp 2012-07-26 20:47:04 UTC (rev 5871)
@@ -0,0 +1,80 @@
+* Charmm Parameter file
+* For 13 bead CG clathrin model
+* Handmade by FXV - 7-21-11
+* Initial guess (very rough)
+
+BONDS
+!
+
+!V(bond) = Kb(b - b0)**2
+!
+!Kb: kcal/mole/A**2
+!b0: A
+!
+!atom type Kb b0
+!
+
+HB PX 0.5 85.5
+PX DT 0.018 135.2
+DT AK 0.045 124.2
+AK LT 0.08 94.1
+
+ANGLES
+!
+!V(angle) = Ktheta(Theta - Theta0)**2
+!
+!Ktheta: kcal/mole/rad**2
+!Theta0: degrees
+!
+!atom types Ktheta Theta0
+!
+PX HB PX 70.0 120.00
+DT PX HB 50.0 144.3
+AK DT PX 35.0 132.6
+LT AK DT 150.0 141.5
+
+DIHEDRALS
+!
+!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
+!
+!Kchi: kcal/mole
+!n: multiplicity
+!delta: degrees
+!
+!atom types Kchi n delta
+!
+X X X X 0.0 1 0.0 ! No dihedrals
+
+IMPROPER
+!
+!V(improper) = Kpsi(psi - psi0)**2
+!
+!Kpsi: kcal/mole/rad**2
+!psi0: degrees
+!note that the second column of numbers (0) is ignored
+!
+!atom types Kpsi psi0
+!
+PX PX HB PX 200.00 0 161.17
+PX HB PX DT 10.0 0 -30.4
+HB PX DT AK 9.5 0 -16.1
+PX DT AK LT 45.0 0 26.1
+
+NONBONDED
+!
+!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
+!
+!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
+!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
+!
+!atom ignored epsilon Rmin/2
+!
+HB 0.000000 HBEPS 43.075000
+PX 0.000000 PXEPS 18.425000
+DT 0.000000 DTEPS 10.455000
+AK 0.000000 AKEPS 25.975000
+LT 0.000000 LTEPS 36.905000
+
+
+END
+
Added: SwiftApps/CMTS/rmsd/input_files/rmsd.temp.tcl
===================================================================
--- SwiftApps/CMTS/rmsd/input_files/rmsd.temp.tcl (rev 0)
+++ SwiftApps/CMTS/rmsd/input_files/rmsd.temp.tcl 2012-07-26 20:47:04 UTC (rev 5871)
@@ -0,0 +1,56 @@
+#====================================
+# THis script will measure the
+# the average angles, bond lengths
+# and dihedral angles.
+#
+# -FXV Oct, 2011
+#===================================
+
+mol delete all
+
+# set atom selection
+set seltext "type HB AK"
+
+# Set the initial frame
+set inifrm 200
+
+set psf cg_clath_cage.psf
+set pdb cg_clath_cage.pdb
+set dcd cg_clath_cage.BLAB1_BLAB2.dcd
+
+# Load input files
+mol load psf $psf
+# Load trajectory
+mol addfile $pdb type pdb
+mol addfile $dcd type dcd first $inifrm last -1 waitfor all
+
+# Get molecule information
+set mol [molinfo top]
+
+# Get the number of frames
+set nmfrm [molinfo $mol get numframes]
+puts "number of frames $nmfrm"
+
+# open rmsd file
+set frmsd [open rmsd.BLAB1_BLAB2.dat w]
+
+# Select atoms
+set ref [atomselect top $seltext frame 0]
+
+# Loop over the number of frames
+for {set ifrm 0} {$ifrm <= $nmfrm} {incr ifrm} {
+
+ set sel [atomselect top $seltext frame $ifrm]
+
+ set irmsd [measure rmsd $ref $sel]
+
+ lappend rmsdlist $irmsd
+
+
+}
+
+# Analysis
+puts $frmsd "B1 B2 [vecmean $rmsdlist]"
+
+exit
+
Added: SwiftApps/CMTS/rmsd/rmsd.sh
===================================================================
--- SwiftApps/CMTS/rmsd/rmsd.sh (rev 0)
+++ SwiftApps/CMTS/rmsd/rmsd.sh 2012-07-26 20:47:04 UTC (rev 5871)
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+b1=$1
+b2=$2
+b1name=$3
+b2name=$4
+namd_input=$5
+namd_parameters=$6
+vmd_script=$7
+
+sed -i -e s/BLAB1/$b1name$b1/ -e s/BLAB2/$b2name$b2/ -e s at __DIR__@$PWD@ $namd_input
+sed -i -e s/HBEPS/-0.01/g -e s/PXEPS/-$b1/g -e s/DTEPS/-$b2/g -e s/AKEPS/-0.01/g -e s/LTEPS/-0.01/g $namd_parameters
+sed -i -e s/BLAB1/$b1name$b1/g -e s/BLAB2/$b2name$b2/g -e s/B1/$b1/ -e s/B2/$b2/ $vmd_script
+
+mpiexec -machinefile $PBS_NODEFILE /Network/Servers/vothfile.uchicago.edu/home/davidk/namd_2.8-intel-openmpi/namd2 $namd_input
+#vmd -dispdev text -e $vmd_script
+mv output/cg_clath_cage.dcd output/cg_clath_cage-$b1-$b2.dcd
Property changes on: SwiftApps/CMTS/rmsd/rmsd.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftApps/CMTS/rmsd/rmsd.swift
===================================================================
--- SwiftApps/CMTS/rmsd/rmsd.swift (rev 0)
+++ SwiftApps/CMTS/rmsd/rmsd.swift 2012-07-26 20:47:04 UTC (rev 5871)
@@ -0,0 +1,36 @@
+type file;
+
+app (file o, file e, file d) rmsd (float b1_val, float b2_val, string b1_name, string b2_name, file namd_input_file, file namd_params_file, file vmd_script_file, file psf_file, file pdb_file)
+{
+ rmsd b1_val b2_val b1_name b2_name @namd_input_file @namd_params_file @vmd_script_file stdout=@o stderr=@e;
+}
+
+# Bead names
+string b1name = "PX";
+string b2name = "DT";
+
+# Bead ranges
+float b1min=0.0;
+float b1max=2.0;
+float b2min=0.0;
+float b2max=2.0;
+
+# Delta
+float delta=0.5;
+
+# Files
+file namd_params <"par_cg_clath.inp">;
+file namd_input <"cg_clath_cage.conf">;
+file vmd_script <"rmsd.temp.tcl">;
+file psf <"cg_clath_cage.psf">;
+file pdb <"cg_clath_cage.pdb">;
+
+foreach b1 in [b1min:b1max:delta] {
+ foreach b2 in [b2min:b2max:delta] {
+ file output <single_file_mapper; file=@strcat("logs/namd-", b1, "-", b2, ".out.txt")>;
+ file error <single_file_mapper; file=@strcat("logs/namd-", b1, "-", b2, ".err.txt")>;
+ file dcd <single_file_mapper; file=@strcat("output/cg_clath_cage-", b1, "-", b2, ".dcd")>;
+ (output, error, dcd) = rmsd(b1, b2, b1name, b2name, namd_input, namd_params, vmd_script, psf, pdb);
+ }
+}
+
Added: SwiftApps/CMTS/rmsd/runrmsd.sh
===================================================================
--- SwiftApps/CMTS/rmsd/runrmsd.sh (rev 0)
+++ SwiftApps/CMTS/rmsd/runrmsd.sh 2012-07-26 20:47:04 UTC (rev 5871)
@@ -0,0 +1,94 @@
+#!/bin/bash
+
+# Usage: swiftopt.sh [-s sitename] [-p paramfile] [-w]
+#
+# NOTE: this command expects symlink "swift" in the cur dir to point
+# to relese installed by setup.sh If you want to run with a different
+# swift release, replace symlink "swift" with a link to your swift
+# release dir.
+
+usage="$0 [-s sitename] [-p paramfile]"
+
+# Function to run Swift
+runswift() {
+ swift -tc.file tc.data -sites.file $1 -config cf rmsd.swift 2>&1 | tee swift.out
+}
+
+# Default settings
+execsite=local
+paramfile=local
+ram=2048M
+
+# Process command line arguments
+while [ $# -gt 0 ]; do
+ case $1 in
+ -s) execsite=$2; shift 2;;
+ *) echo $usage 1>&2
+ exit 1;;
+ esac
+done
+
+# Create next unique run id and run directory
+rundir=$( echo run??? | sed -e 's/^.*run//' | awk '{ printf("run%03d\n", $1+1)}' )
+
+# Exit if rundir already exits. Something is funky
+if [ -d $rundir ];
+then
+ echo "$rundir already exists! exiting." >&2
+ exit 2
+else
+ mkdir $rundir
+fi
+
+# Copy input files
+cp input_files/* $rundir
+echo Run directory $rundir: site=$execsite paramfile=$paramfile
+
+# Report an error if configuration files are missing
+if [ ! -f "conf/$execsite.xml" ] && [ ! -f "conf/$execsite.conf" ]; then
+ echo Unable to find requested configuration file for site $execsite
+ exit 1
+fi
+
+# Use start-coaster-service if site is a .conf file
+if [ -f "conf/$execsite.conf" ]; then
+ USE_SCS=1
+fi
+
+# Check for missing .cf files
+if [ -f "conf/$execsite.xml" ] && [ ! -f "conf/$execsite.cf" ]; then
+ echo Missing configuration file $execsite.cf
+fi
+
+# Do the run
+cd $rundir
+cp ../rmsd.swift .
+export WORK=$PWD/swiftwork
+mkdir -p $PWD/swiftwork/workers
+
+# Use start-coaster-service if the site uses a .conf file
+if [ "$USE_SCS" == "1" ]; then
+ cp ../conf/$execsite.conf coaster-service.conf
+ cp ../conf/$execsite.cf cf
+ sed -i -e "s at _RUNDIR_@$rundir@" coaster-service.conf
+ start-coaster-service
+fi
+
+# Run gensites
+if [ ! "$USE_SCS" == 1 ]; then
+ cp ../conf/$execsite.cf cf
+ gensites -p ../conf/$execsite.cf ../conf/$execsite.xml > $execsite.xml
+fi
+
+echo "Run dir=$rundir" >> ABOUT
+echo "Work dir=$WORK" >> ABOUT
+echo "Total jobs=$total_jobs" >> ABOUT
+
+if [ "$USE_SCS" == "1" ]; then
+ runswift "sites.xml"
+ stop-coaster-service
+else
+ runswift "$execsite.xml"
+fi
+
+exit
Property changes on: SwiftApps/CMTS/rmsd/runrmsd.sh
___________________________________________________________________
Added: svn:executable
+ *
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