Re: RBCG water simulation

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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