From: Chris Harrison (charris5_at_gmail.com)
Date: Fri May 27 2011 - 12:49:08 CDT
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
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