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.
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:21 CST