Team:EPF-Lausanne/Modeling/NamdConf

 

=Job description= This section is needed are we trying to keep track of each run, please put type of simulation, pdb loaded, date, time and your name
 * ## JOB DESCRIPTION                                        ##
 * # NPT simul
 * # 2v0u in a water box
 * # 12.08.09
 * # 14:00
 * # Nicolas Gobet
 * # 14:00
 * # Nicolas Gobet

=Adjustable parameters=

First run
This is an example for the heating.
 * ## ADJUSTABLE PARAMETERS                                  ##
 * ## ADJUSTABLE PARAMETERS                                  ##


 * structure         ./2v0up_wb_i.psf
 * coordinates       ./2v0up_wb_i.pdb


 * set paramfich   ./common/par_all27_prot_lipid-fmn_dark.prm


 * set temperature   300


 * #initial temperature
 * temperature        $temperature


 * set outputdir       ./output_eq3


 * set outputname      $outputdir/2v0up_wb_i_eq
 * set outputmin       $outputdir/min
 * set outputheating   $outputdir/heating
 * set outputnpt1      $outputdir/NPT_1
 * set outputnvt       $outputdir/NVT_1
 * set outputnpt2      $outputdir/NPT_2

Resume from .coord, .vel, .xsc
This is to resume from .coor, .vel and .xsc files. As we load velocities and positions from a file, we don't have to set initial temperature, load .pdb for postions of the atoms and set parameters such as box size
 * ## ADJUSTABLE PARAMETERS                                  ##
 * ## ADJUSTABLE PARAMETERS                                  ##


 * structure         ./2v0up_wb_i.psf
 * set paramfich   ./common/par_all27_prot_lipid-fmn_dark.prm


 * set temperature 300


 * set inputdir       ./output_eq2
 * set inputname      2v0up_wb_i_eq


 * coordinates 	$inputdir/$inputname.coor
 * velocities	$inputdir/$inputname.vel
 * extendedSystem $inputdir/$inputname.xsc


 * set outputdir       ./output_sim2


 * set outputname      $outputdir/2v0up_wb_i_sim
 * set outputsim       $outputdir/min

=Simulation parameters=

First run
This part is from a heating .conf. The size of the box and origin has to be adjusted. PMEGridSize parameters have to be adjusted to be higher than the size of the box and be a multiple of 2, 3 and 5. (please refer to tutorial)
 * ## SIMULATION PARAMETERS                                  ##
 * ## SIMULATION PARAMETERS                                  ##


 * firsttimestep     0


 * # Input
 * paraTypeCharmm	   on
 * parameters         $paramfich


 * # Force-Field Parameters
 * exclude            scaled1-4
 * 1-4scaling         1.0
 * cutoff             12.
 * switching          on
 * switchdist         10.
 * pairlistdist       13.5


 * # Integrator Parameters
 * # We use timestep of 2.0 only for heating!!!!!! Any other case is 1.0
 * timestep           2.0
 * rigidBonds         all  ;# needed for 2fs steps
 * nonbondedFreq      1
 * fullElectFrequency 2
 * stepspercycle      10


 * # Constant Temperature Control
 * langevin           on    ;# do langevin dynamics
 * langevinDamping    $temperature     ;# damping coefficient (gamma) of 5/ps
 * langevinTemp       $temperature # je viens de changer, foiruex avant
 * langevinHydrogen   off    ;# don't couple langevin bath to hydrogens


 * # Periodic Boundary Conditions
 * cellBasisVector1   63.39    0.   0.
 * cellBasisVector2    0.   65.404   0.
 * cellBasisVector3    0.    0   69.675
 * cellOrigin         14.1049346924   3.42041158676  3.65775823593


 * wrapAll            on


 * # PME (for full-system periodic electrostatics)
 * PME                yes
 * PMEGridSizeX       66
 * PMEGridSizeY       66
 * PMEGridSizeZ       70


 * # Constant Pressure Control (variable volume)
 * useGroupPressure     yes ;# needed for rigidBonds
 * useFlexibleCell      no ;# no for water box
 * useConstantArea      no ;# no for water box


 * langevinPiston       on
 * langevinPistonTarget 1.01325 ;#  in bar -> 1 atm
 * langevinPistonPeriod 200.
 * langevinPistonDecay  100.
 * langevinPistonTemp   $temperature


 * # Output
 * outputName         $outputname


 * restartfreq        500     ;# 500steps = every 1ps
 * dcdfreq            200
 * xstFreq            200
 * outputEnergies     200
 * outputPressure     200
 * outputTiming  	    200
 * binaryoutput	   off

Resume from .coord, .vel, .xsc
The only difference here is that we lower timestep for NPT simulation to copy parameters from Schulten's paper. Then, we don't set the size of the water box as it is loaded from the file and we lower the frequency of output. This is what you have to copy for a NPT simulation.
 * ## SIMULATION PARAMETERS                                  ##
 * ## SIMULATION PARAMETERS                                  ##


 * firsttimestep     0


 * # Input
 * paraTypeCharmm	   on
 * parameters         $paramfich


 * # Force-Field Parameters
 * exclude            scaled1-4
 * 1-4scaling         1.0
 * cutoff             12.
 * switching          on
 * switchdist         10.
 * pairlistdist       13.5


 * # Integrator Parameters
 * timestep           1.0
 * rigidBonds         all  ;# needed for 2fs steps
 * nonbondedFreq      1
 * fullElectFrequency 2
 * stepspercycle      10


 * # Constant Temperature Control
 * langevin           on    ;# do langevin dynamics
 * langevinDamping    $temperature     ;# damping coefficient (gamma) of 5/ps
 * langevinTemp       $temperature # je viens de changer, foiruex avant
 * langevinHydrogen   off    ;# don't couple langevin bath to hydrogens


 * # Periodic Boundary Conditions
 * wrapAll            on


 * # PME (for full-system periodic electrostatics)
 * PME                yes
 * PMEGridSizeX       50
 * PMEGridSizeY       54
 * PMEGridSizeZ       60


 * # Constant Pressure Control (variable volume)
 * useGroupPressure     yes ;# needed for rigidBonds
 * useFlexibleCell      no ;# no for water box
 * useConstantArea      no ;# no for water box


 * langevinPiston       on
 * langevinPistonTarget 1.01325 ;#  in bar -> 1 atm
 * langevinPistonPeriod 200.
 * langevinPistonDecay  100.
 * langevinPistonTemp   $temperature


 * # Output
 * outputName         $outputname


 * restartfreq        2000     ;# 500steps = every 1ps
 * dcdfreq            2000
 * xstFreq            2000
 * outputEnergies     2000
 * outputPressure     2000
 * outputTiming  	    2000
 * binaryoutput	   off

=Execution script=

Heating

 * ## EXECUTION SCRIPT                                       ##
 * ## EXECUTION SCRIPT                                       ##


 * # run one step to get into scripting mode
 * minimize 0


 * # turn off until later
 * langevinPiston	off


 * # Minimization
 * minimize           2500
 * reinitvels         5
 * output $outputmin


 * # heating NPT
 * # langevin	on
 * for {set i 5} {$i <= $temperature} {incr i 5} {			;# i = 5, $i<300, incr i = 5
 * set temperaturei $i
 * langevinTemp $temperaturei
 * langevinPistonTemp $temperaturei
 * run 2000						;# run 2000
 * }


 * #to be sure we are at the right temperature
 * langevinTemp $temperature
 * langevinPistonTemp $temperature


 * output $outputheating


 * # 1st equilibrate pression
 * # NPT equilibration
 * # langevin on
 * langevinPiston on
 * run 50000						;# run 50000
 * output $outputnpt1


 * # NVT equilibration
 * # langevin off
 * langevinPiston	off
 * run 50000						;# run 50000
 * output $outputnvt


 * # NPT equilibration
 * langevinPiston	on
 * run 150000						;# run 150000
 * output $outputnpt2

NPT run

 * ## EXECUTION SCRIPT                                       ##
 * ## EXECUTION SCRIPT                                       ##


 * # run one step to get into scripting mode
 * #minimize 0


 * # NPT equilibration
 * # langevin	on
 * #langevinPiston	on
 * run 1000000						;# run 1 ns
 * output $outputsim



