[Swift-commit] r6579 - SwiftTutorials/CMTS_2013-06-17/namd_sweep

[wilde at ci.uchicago.edu]

Author: wilde
Date: 2013-06-17 14:37:38 -0500 (Mon, 17 Jun 2013)
New Revision: 6579

Modified:
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.temp.conf
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.temp.tcl
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml
Log:
Updates for faster namd runs with correct vmd extraction.  Changes initfrm and drops minimize.

Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.temp.conf
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.temp.conf	2013-06-17 19:37:11 UTC (rev 6578)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.temp.conf	2013-06-17 19:37:38 UTC (rev 6579)
@@ -84,7 +84,7 @@
 #langevinTemp $temperature
 
 
-minimize            10000
+#minimize            10000
 #reinitvels          $temperature
 #run 		    1000000 desired, 200000 min to get non-zero RMSDs
-run                 20000
+run                 10000

Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.temp.tcl
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.temp.tcl	2013-06-17 19:37:11 UTC (rev 6578)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.temp.tcl	2013-06-17 19:37:38 UTC (rev 6579)
@@ -13,6 +13,7 @@
 
 # Set the initial frame
 set inifrm 200
+set inifrm 1
 
 set psf cg_clath_cage.psf
 set pdb cg_clath_cage.pdb

Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml	2013-06-17 19:37:11 UTC (rev 6578)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml	2013-06-17 19:37:38 UTC (rev 6579)
@@ -16,9 +16,9 @@
 
     <!-- Set number of jobs and nodes per job here: -->
     <profile namespace="globus" key="slots">1</profile>
-    <profile namespace="globus" key="maxnodes">2</profile>
-    <profile namespace="globus" key="nodegranularity">2</profile>
-    <profile namespace="karajan" key="jobThrottle">.03</profile>
+    <profile namespace="globus" key="maxnodes">1</profile>
+    <profile namespace="globus" key="nodegranularity">1</profile>
+    <profile namespace="karajan" key="jobThrottle">.15</profile>
 
     <!-- Set estimated app time (maxwalltime) and requested job time (maxtime) here: -->
     <profile namespace="globus" key="maxWalltime">00:15:00</profile>