Tutorial-l Mailing List

From: javacfish (javacfish_at_yahoo.com.cn)
Date: Tue Apr 17 2012 - 11:18:30 CDT

Hi all, What is the means of the function of get_first_ts in the Residue-Based Coarse tutorial (http://www.ks.uiuc.edu/Training/Tutorials/) as below. It seems no usefulness. Who can tell me about its function? Thanks   ############################################################ proc get_first_ts { xscfile } {   set fd [open $xscfile r]   gets $fd   gets $fd   gets $fd line   set ts [lindex $line 0]   close $fd   return $ts } ############################################################# ## JOB DESCRIPTION                                         ## ############################################################# # # Initial minimization of the coarse-grained system. # ############################################################# ## ADJUSTABLE PARAMETERS                                   ## ############################################################# #set inputname       set outputname  system-min set restart 0 set temperature    310 cosAngles          on structure ../02-solvate-ionize/example-output/02-ionize.psf  coordinates ../02-solvate-ionize/example-output/02-ionize.pdb temperature      $temperature firsttimestep   0   ############################################################# ## SIMULATION PARAMETERS                                   ##  ############################################################# # Input paraTypeCharmm    on parameters          ../04-cgc-top-par-files/martini-par/martini-protein-bonds.par parameters          ../04-cgc-top-par-files/martini-par/martini-protein-angles-cos.par parameters          ../04-cgc-top-par-files/martini-par/martini-protein-dihedrals.par parameters          ../04-cgc-top-par-files/martini-par/martini-all-nonb.par parameters   ../04-cgc-top-par-files/martini-par/martini-lipids-bonds-angles-dihedrals.par # Force-Field Parameters exclude             1-2 1-4scaling          1.0 cutoff              12.0 martiniSwitching    on switching           on PME    off switchdist          9.0 pairlistdist        14.0 dielectric          15.0 # Integrator Parameters timestep            20.0 nonbondedFreq       1  stepspercycle       10 # Constant Temperature Control langevin            yes    ;# do langevin dynamics langevinDamping     1      ;# damping coefficient (gamma) of 1/ps langevinTemp        $temperature langevinHydrogen    off    ;# don't couple langevin bath to hydrogens # Periodic Boundary Conditions if {1} { cellBasisVector1   126.788  0       0 cellBasisVector2   0       129.075  0 cellBasisVector3   0       0        79.0 cellOrigin         0.19492866098880768 0.18127670884132385 0.6883298754692078 } wrapAll             on # Constant Pressure Control (variable volume) useGroupPressure      no useFlexibleCell       yes useConstantArea       no useConstantRatio      yes langevinPiston        yes langevinPistonTarget  1.01325 ;#  in bar -> 1 atm langevinPistonPeriod  2000.  #usually 2000 for RBCG system  langevinPistonDecay   1000.  #usually 1000 for RBCG system langevinPistonTemp    $temperature # Output outputName          $outputname restartfreq          1000    dcdfreq              1000 xstFreq              1000 outputEnergies       100 outputPressure       100 ############################################################# ## EXECUTION SCRIPT                                        ## ############################################################# if {$restart == 0} { minimize             5000 reinitvels          $temperature } ############################################################ Javacfish
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