[gmx-developers] dispersion correction / exploding box

[Rainer Böckmann]

Dear David,

the dispersion energy is quite high, starting at 5*10**4 and decreasing with
increasing box volume to ~3*10**4 within 70ps (d=1.5nm between protein and box).
A similar simulation with d=1.2nm with stable volume shows a dispersion energy
of -1*10**4.

Other parameters:
 RUN CONTROL PARAMETERS =
integrator               = md
; start time and timestep in ps =
tinit                    = 0
dt                       = 0.002
nsteps                   = 50000
; mode for center of mass motion removal =
comm-mode                = Linear
; number of steps for center of mass motion removal =
nstcomm                  = 1
; group(s) for center of mass motion removal =
comm-grps                =

; LANGEVIN DYNAMICS OPTIONS =
; Temperature, friction coefficient (amu/ps) and random seed =
bd-temp                  = 310
bd-fric                  = 0
ld_seed                  = 1993

; ENERGY MINIMIZATION OPTIONS =
; Force tolerance and initial step-size =
emtol                    = 0.000001
emstep                   = 0.01
; Max number of iterations in relax_shells =
niter                    = 100
; Step size (1/ps^2) for minimization of flexible constraints =
fcstep                   = 0
; Frequency of steepest descents steps when doing CG =
nstcgsteep               = 1000

; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout                  = 10000
nstvout                  = 10000
nstfout                  = 0
; Output frequency for energies to log file and energy file =
nstlog                   = 500
nstenergy                = 500
; Output frequency and precision for xtc file =
nstxtcout                = 500
xtc_precision            = 1000
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps                 =
; Selection of energy groups =
energygrps               =

; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist                  = 10
; ns algorithm (simple or grid) =
ns_type                  = grid
; Periodic boundary conditions: xyz or no =
pbc                      = xyz
; nblist cut-off         =
rlist                    = 1
domain-decomposition     = no

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype              = PME
rcoulomb_switch          = 0
rcoulomb                 = 1.0
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r                = 1
; Method for doing Van der Waals =
vdw-type                 = Cut-off
; cut-off lengths        =
rvdw_switch              = 0
rvdw                     = 1.0
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr                 = EnerPres
; Spacing for the PME/PPPM FFT grid =
fourierspacing           = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
; EWALD/PME/PPPM parameters =
pme_order                = 4
ewald_rtol               = 1e-05
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = no

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
Tcoupl                   = yes
; Groups to couple separately =
tc_grps                  = Protein Other
; Time constant (ps) and reference temperature (K) =
tau_t                    = 0.1 0.1
ref_t                    = 310 310
; Pressure coupling      =
Pcoupl                   = Berendsen
Pcoupltype               = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0

; OPTIONS FOR BONDS     =
constraints              = h-bonds
; Type of constraint algorithm =
constraint_algorithm     = Lincs
; Do not constrain the start configuration =
unconstrained_start      = no
; Use successive overrelaxation to reduce the number of shake iterations =
Shake-SOR                = no
; Relative tolerance of shake =
shake_tol                = 1e-04
; Highest order in the expansion of the constraint coupling matrix =
lincs_order              = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle          = 30
; Convert harmonic bonds to morse potentials =
morse                    = no


Best,
Rainer

Quoting David <spoel at xray.bmc.uu.se>:

> On Mon, 2005-08-22 at 18:42 +0200, Rainer Böckmann wrote:
> > Dear All:
> > 
> > we experienced a very fast (~10-50ps) increasing/exploding box for a 
> > system of approx. 100,000 atoms using the OPLS forcefield, TIP4 water, 
> > and a dodecahedron box aready during position restraint runs (restraints 
> > on the protein). Further options:
> > 
> > gromacs 3.3, cvs version (download ~3 weeks ago)
> > PME
> > energy/pressure dispersion correction switched on
> > 310 K, 1bar
> > 
> > We observe this behaviour only for certain box sizes/proteins, e.g. the 
> > box explodes using a distance of 1.4nm or 1.5nm  between the protein and 
> > the box but not for 1.2nm. It is not dependent on the PME parameters, 
> > but at least partly on the dispersion correction term. The box appears 
> > to be stable without the dispersion correction.'
> 
> Can you give more details? Dispersion energy, VDW treatment and cut-offs
> etc.
> 
> > 
> > Any ideas?
> > 
> > Thanks & best wishes,
> > Rainer
> > 
> -- 
> David.


__________________________________________________________
Dr. Rainer Böckmann
Theoretical & Computational Membrane Biology
Center for Bioinformatics Saar
Universität des Saarlandes
Gebäude 17.1, EG
D-66041 Saarbrücken, Germany
Phone: ++49 +681 302-64169  FAX: ++49 +681 302-64180
E-Mail: rainer at bioinformatik.uni-saarland.de
http://www.bioinf.uni-sb.de/RB/
___________________________________________________________


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