Re: follow up question about heating the system

From: surendra negi (negi009_at_yahoo.com)
Date: Wed Feb 15 2006 - 16:18:30 CST

Yeah, It is standard conf file for namd. you can run
it using bsub like bsub < file.conf or like usual namd
command line like namd file.conf > file.log etc.

--- patrick wintrode <pat_wde2_at_yahoo.com> wrote:

> Thanks for the sample script.
>
> Is this tcl script or a regular .conf file? I'm
> running this as a batch job on a remote machine.
> Will NAMD automatically recognize tcl commands in
> the configuration file?
>
> Thanks again.
>
> Patrick L. Wintrode
>
> surendra negi <negi009_at_yahoo.com> wrote: Try to use
> following procedure.. change the paramter
> marked with xxx and also minimization as well as MD
> steps as per your requirement. I hope this will
> work.
> surendra
> ------------
>
> #
> # Input files
>
> set MOL solvated
> structure ${MOL}_ionised.psf
>
> #after minimization
>
> set inprot ${MOL}_ionised_min
> coordinates ${inprot}.coor
> extendedSystem ${inprot}.xsc
>
> # Input Force-Field Parameters
>
> paraTypeCharmm on
> parameters par_all27_prot_lipid.inp
>
> #
> # Output files & writing frequency for DCD
> # and restart files
> #
>
> outputname output/solvated_heat_out
> binaryoutput off
> restartfreq 1000
> binaryrestart yes
> dcdFile output/solvated_heat_out.dcd
>
> #
> # Frequencies for logs and the xst file
> #
> outputEnergies 1000
> outputTiming 1000
> outputPressure 1000
> xstFreq 1000
> dcdFreq 1000
>
> #
> # Timestep & friends
> #
>
> timestep 2.0 ;# 2fs/step
> nonbondedFreq 2
> rigidBonds all
> rigidTolerance 0.00000001
> fullElectFrequency 4
> stepspercycle 20
>
>
> #
> # Simulation space partitioning
> #
> switching on
> switchDist 10
> cutoff 12
> pairlistdist 13.5
>
> #
> # Basic dynamics
> #
> temperature 0
> COMmotion no
> dielectric 1.0
> exclude scaled1-4
> 1-4scaling 1.0
>
>
> #
> # Particle Mesh Ewald parameters.
> #
>
> PME yes
> PMEGridSizeX xx
> PMEGridSizeY xx
> PMEGridSizeZ xx
>
> #
> # Periodic boundary things
> #
> wrapWater on
> wrapNearest on
> wrapAll on
>
> margin 1
>
>
> cellBasisVector1 xx 0. 0.
> cellBasisVector2 0. xx 0.
> cellBasisVector3 0. 0. xx
> cellOrigin xx xx xx
>
> #
> # Fixed atoms for initial heating-up steps
> #
> fixedAtoms on
> fixedAtomsForces on
> fixedAtomsFile fix_backbone.pdb
> fixedAtomsCol B
>
> #
> # Restrained atoms for initial heating-up steps
> #
> constraints on
> consRef restrain_ca.pdb
> consKFile restrain_ca.pdb
> consKCol B
>
> #
> # Langevin dynamics parameters
> #
> langevin on
> langevinDamping 10
> langevinTemp 310 #
> langevinHydrogen on
>
> langevinPiston on
> langevinPistonTarget 1.01325
> langevinPistonPeriod 200
> langevinPistonDecay 100
> langevinPistonTemp 310 #
>
> useGroupPressure yes
>
>
> # The actual minimisation and heating-up
>
> # run one step to get into scripting mode
> minimize 0
>
> # turn off pressure control until later
> langevinPiston off
>
> # minimize nonbackbone atoms
> minimize 100000
> ;#
> output output/min_fix
>
> #
> # min all atoms
> #
> fixedAtoms off
> minimize 100000
> ;#
> output output/min_all
>
> #
> # heat with Ps restrained
> #
> set temp 10;
> while { $temp < 311 } { ;#
> langevinTemp $temp
> run 5000 ;#
> output output/heat_P
> set temp [expr $temp + 31]
> }
>
> #
> # equilibrate volume with Ps restrained
> #
> langevinPiston on
> run 100000
> ;#
> output output/equil_P
>
> #
> # equilibrate volume without restraints
> #
> constraintScaling 0
> run 100000 ;#
>
>
>
> --- patrick wintrode
> wrote:
>
> > Hi all,
> >
> > I'm trying to minimize my system and then slowly
> > heat it to 310 degrees C. After 2000 minimization
> > steps I run dynamics for 10,000 steps. The
> > temperature is set to 0 and langevin dynamics and
> > langevin piston are both turned off.
>
=== message truncated ===

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