Re: RBCG water simulation

From: Cristhian Boetsch (cristhian.boetsch_at_gmail.com)
Date: Fri Jun 03 2011 - 07:22:38 CDT

SOLVED, at least, it seems to work, I don't know enough why, but with
Nosé-Hoover langevin piston doesn't work, so I tried with the
BerendsenPressure on comand, and now the density of my simulation is about
0.98 - 0.99

2011/5/27 Chris Harrison <charris5_at_gmail.com>

> Cristhian,
>
> Can you send me your input files, off list?
>
> Best,
> Chris
>
>
> On Fri, May 27, 2011 at 12:17 PM, Cristhian Boetsch
> <cristhian.boetsch_at_gmail.com> wrote:
> > Hi all:
> > I run a coarse grain MD.
> > Because it is the first time I run one of this type of dynamics, I worked
> > with a water box about 30 x 30 x 30 A^3,
> > using the parameter file provide in de cgtools plugin from vmd.
> > I first minimize it, make a short run with langevinPiston off, and then I
> > turn the last one "on", and I run a few more steps.
> > The fact is, as the piston turn on, the volumen of my water-box increase
> > almost 100 times:
> >
> > - At the begining:
> > mass 34344 uma 5,705E-020 g
> > volume 19479048,7792 A^3 1,948E-017 cm^3
> > density 0,0029288 g/cm^3
> >
> > - and the last step computed:
> > volume 24809,5 A^3 2,481E-020 cm^3
> > density 2,2995 g/cm^3
> >
> > This is my config file:
> >
> > # Force-Field Parameters
> > exclude none
> > cutoff 12.0
> > switching on
> > switchdist 9.0
> > pairlistdist 14.5
> >
> > # Integrator Parameters
> > timestep 10.0 ;# 1fs/step (2)
> > nonbondedFreq 1
> > fullElectFrequency 2
> > stepspercycle 20
> >
> > # Constant Temperature Control
> > langevin on ;# do langevin dynamics
> > langevinDamping 1 ;# damping coefficient (gamma) of 10/ps (5)
> > langevinTemp 310
> > langevinHydrogen yes ;# don't couple langevin bath to hydrogens
> >
> >
> > langevinPiston on
> > langevinPistonTarget 1.01325
> > langevinPistonPeriod 1000
> > langevinPistonDecay 500
> > langevinPistonTemp 310
> >
> > useGroupPressure yes
> > useFlexibleCell no
> > useConstantRatio no
> >
> > # Periodic Boundary Conditions
> > cellBasisVector1 29.0 0.0 0.0
> > cellBasisVector2 0.0 29.5 0.0
> > cellBasisVector3 0.0 0.0 29.0
> > cellOrigin 0.000 0.000 0.000
> > margin 2
> >
> > wrapAll on
> > -----------------
> >
> > but when I coment the nbfix term:
> > !P P -1.195 5.3
> > so it uses the L-J term (P 0.000000 -1.195 2.35 !)
> >
> > or set de Rmin at half of its value (2.65), the density is more
> reasonable
> > (1.5 - 2.1 respectively).
> > I've read in the main list problems in the minimations in a cg-model, and
> > otherones
> > with nbfix term in all atom simulations.
> > Someone could help me?
> >
> > Thanks, Cristhian
> >
> >
>
>
>
> --
> Chris Harrison, Ph.D.
> Theoretical and Computational Biophysics Group
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>
> char_at_ks.uiuc.edu Voice: 217-244-1733
> http://www.ks.uiuc.edu/~char Fax: 217-244-6078
>

-- 
Mic. Cristhian Boetsch
Universidad Nacional de Río Cuarto
Río Cuarto - Argentina
Cel.: 0358-154361332

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