From: Aron Broom (broomsday_at_gmail.com)
Date: Sun Jul 15 2012 - 20:31:26 CDT
what do you mean by missing? Do you mean that if you open up the output
NE2_gbis_eq.coor file, the file is empty?
On Sun, Jul 15, 2012 at 6:13 PM, Roy Fernando <roy.nandos_at_gmail.com> wrote:
> Dear All,
>
> I try to simulate my test system containing two Neon atom under
> Generalized Born Implicit Solvent Technique.
> I did not use any charge.
> At the end of the equilibration, I observe that the atoms are missing.
> I used the basic configuration file came with the tutorial. (posted below).
> I will appreciate if someone can give some insight on how I can keep the
> atoms confined to a certain volume. Or is it not possible in this method?
>
> regards,
>
> Roy
>
> #############################################################
> ## JOB DESCRIPTION ##
> #############################################################
>
> # Minimization and Equilibration of
> #Neon atoms in generalized Born implicit solvent
>
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> structure NE2-1.psf
> coordinates NE2-1.pdb
>
> set temperature 310
> set outputname NE2_gbis_eq
>
> firsttimestep 0
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters par_all27_prot_lipid.inp
> temperature $temperature
>
> # Implicit Solvent
> gbis on
> alphaCutoff 2.0
> ionConcentration 0.0
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 4.0
> switching on
> switchdist 3.0
> pairlistdist 6.0
>
>
> # Integrator Parameters
> timestep 2.0 ;# 2fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
> langevinTemp $temperature
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>
> # Output
> outputName $outputname
>
> restartfreq 500 ;# 500steps = every 1ps
> dcdfreq 250
> xstFreq 250
> outputEnergies 100
> outputPressure 100
>
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> minimize 1000
> reinitvels $temperature
>
> run 25000 ;# 5ps
>
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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