Re: Script Help

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun May 29 2011 - 18:58:44 CDT

On Sun, May 29, 2011 at 7:16 PM, flavio seixas <oivalf_nix_at_yahoo.com> wrote:
> Hi people.
>
> I am trying to run a slow cooling simulate annealing, in which I rapidly rise te temperature to 1000K or 2000K and slowly down to 300K in steps of -25K.

cooling by 25K over 1000 MD steps is not exactly a slow cooling.
it is indeed very rapid.

> I am using the script below that I found in namd-list but without sucess. The temperature only rises slowly, but dont turns to fall.
>
> Could someone tells me what I am doing wrong?

you have to give the thermostat time to readjust the temperature.
particularly, if you initialize to 300K instead of 2000K without any
significant equilibration time.

cheers,
      axel.

> I will be gratefull for any help.
>
> Flavio
>
> #############################################################
> ## ADJUSTABLE PARAMETERS                                   ##
> #############################################################
>
> structure          PROT_wb.psf
> coordinates        PROT_wb.pdb
>
> set temperature    300
> set outputname     PROT_wb_eq
>
> firsttimestep      0
>
>
> #############################################################
> ## SIMULATION PARAMETERS                                   ##
> #############################################################
>
> # Input
> paraTypeCharmm      on
> parameters          par_all27_prot_lipid_na.inp
> temperature         $temperature
>
>
> # Force-Field Parameters
> exclude             scaled1-4
> 1-4scaling          1.0
> cutoff              12.0
> switching           on
> switchdist          10.0
> pairlistdist        13.5
>
>
> # Integrator Parameters
> timestep            1.0  ;# 1fs/step
> rigidBonds          all  ;# needed for 2fs steps
> nonbondedFreq       1
> fullElectFrequency  2
> stepspercycle       10
>
>
> # Constant Temperature Control
> langevin            on    ;# do langevin dynamics
> langevinDamping     5     ;# damping coefficient (gamma) of 5/ps
> langevinTemp        $temperature
> langevinHydrogen    off    ;# don't couple langevin bath to hydrogens
>
>
> # Periodic Boundary Conditions
> cellBasisVector1    86.     0.    0.
> cellBasisVector2     0.   100.5   0.
> cellBasisVector3     0.     0.   76.0
> cellOrigin          70.0   48.0  64.0
>
> wrapAll             on
>
>
> # PME (for full-system periodic electrostatics)
> PME                 yes
> PMEGridSpacing      1.0
>
> #manual grid definition
> #PMEGridSizeX        90
> #PMEGridSizeY       105
> #PMEGridSizeZ        80
>
>
> # Constant Pressure Control (variable volume)
> useGroupPressure      yes ;# needed for rigidBonds
> useFlexibleCell       no
> useConstantArea       no
>
> langevinPiston        on
> langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
> langevinPistonPeriod  100.0
> langevinPistonDecay   50.0
> langevinPistonTemp    $temperature
>
>
> # Output
> outputName          $outputname
> binaryoutput        no
>
>
> restartfreq         500     ;# 500steps = every 1ps
> dcdfreq             250
> xstFreq             250
> outputEnergies      100
> outputPressure      100
>
>
> #############################################################
> ## EXTRA PARAMETERS                                        ##
> #############################################################
>
>
> #############################################################
> ## EXECUTION SCRIPT                                        ##
> #############################################################
>
> # Minimization
> minimize   100
>
> reassignTemp 1000
>
> run 500
> for { set TEMP 1000 } { $TEMP >= 300 } { incr TEMP -25 } {
>  reassignTemp $TEMP
>  run 1000
> }
>
> minimize 100
>
>
>
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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