From: javacfish (javacfish_at_yahoo.com.cn)
Date: Fri Apr 20 2012 - 01:17:57 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
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:21:53 CST