RBCG water simulation

From: Cristhian Boetsch (cristhian.boetsch_at_gmail.com)
Date: Fri May 27 2011 - 12:17:38 CDT

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

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