From: Ramya Gamini (ramyabhargavi_at_gmail.com)
Date: Fri Apr 20 2012 - 14:32:41 CDT
Hi,
You are right. I has no usefulness. Its only used if you are using the
configuration to restart your simulation.
Then the function with other lines (not mentioned in this config
file), may be used to get the firsttimestep from your previous run
restart.xsc flle
cheers,
Ramya
On Fri, Apr 20, 2012 at 1:17 AM, javacfish <javacfish_at_yahoo.com.cn> wrote:
> 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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