Re: What is the means of system-min.conf in the Residue-Based Coarse tutorial?

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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