[gmx-users] pathologically expanding box

[Berk Hess]

Hi,

I think the problem is epsilon_r=80, which reduces your electrostatics interactions
by a factor of 80.

Berk

> Date: Mon, 13 Dec 2010 17:46:14 -0500
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] pathologically expanding box
> 
> 
> 
> Greg Bowman wrote:
> > Hello,
> > 
> > Has anyone else experienced a pathologically expanding box during 
> > equilibration in the NPT ensemble?  I've solvated my system with 
> > editconf/genbox, energy minimized, equilibrated in NVT with the protein 
> > coordinates restrained, and then equilibrated in NPT without any 
> > position restraints.  During the NPT equilibration all the box 
> > dimensions are doubling and the density decreases drastically.
> > 
> > I'm using the v-rescale thermostat and the Berendsen barostat in gromacs 
> > 4.5.3 with the AMBER03 force field and tip3p water.  I've also tried 
> > OPLSAA with SPC water, a number of different box types (cubic, 
> > octahedral, dodecahedral), and shorter tau_t and tau_p settings.  I also 
> > tried adding another energy minimzation step between my NVT and NPT phases.
> > 
> 
> Is the temperature, potential energy, etc. stable after NVT?
> 
> Is the increase in box size steady, oscillating, or sudden?
> 
> Does the problem persist with different combinations of thermostat and barostat, 
> or is it limited to V-rescale + Berendsen?
> 
> -Justin
> 
> > My mdp settings for the NPT ensemble are below.
> > 
> > Thanks for your help.
> > 
> > Greg
> > 
> > ; RUN CONTROL PARAMETERS
> > ;define              = -DPOSRES
> > integrator          = md
> > tinit               = 0
> > nsteps              = 50000
> > dt                  = 0.002000
> > comm-mode           = linear
> > nstcomm             = 4
> > 
> > ; CONSTRAINTS
> > constraints         = all-bonds
> > lincs_order         = 6
> > lincs_iter          = 2
> > 
> > ; NEIGHBORSEARCHING PARAMETERS
> > ns_type             = grid
> > nstlist             = 4
> > rlist               = 1.2
> > pbc                 = xyz
> > 
> > ; ELECTROSTATICS
> > coulombtype         = pme ;-switch
> > rcoulomb            = 1.2
> > ;rcoulomb-switch     = 0.800000
> > fourierspacing      = 0.120000
> > fourier_nx          = 0
> > fourier_ny          = 0
> > fourier_nz          = 0
> > pme_order           = 6
> > ewald_rtol          = 0.000001
> > ewald_geometry      = 3d
> > epsilon_surface     = 0
> > optimize_fft        = yes
> > epsilon_r           = 80
> > 
> > ; VDW
> > vdw-type            = switch
> > rvdw                = 1.2
> > rvdw-switch         = 1.1
> > DispCorr            = EnerPres
> > 
> > ; OUTPUT CONTROL OPTIONS
> > ; Output frequency for coords (x), velocities (v) and forces (f) =
> > nstxout             = 0
> > nstvout             = 0
> > nstfout             = 0
> > nstlog              = 0
> > energygrps          = System
> > nstenergy           = 100
> > nstcalcenergy       = 1
> > nstxtcout           = 0
> > xtc-grps            = Protein
> > 
> > Tcoupl              = v-rescale
> > tau_t               = 0.5
> > tc-grps             = System
> > ref_t               = 300
> > ld_seed             = -1
> > 
> > Pcoupl              = berendsen
> > Pcoupltype          = isotropic
> > tau_p               = 5
> > compressibility     = 4.5e-5
> > ref_p               = 1.0
> > 
> > gen_vel             = yes
> > gen_temp            = 300.0
> > gen_seed            = -1
> > 
> > 
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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