[gmx-users] bk3 water energy minimization potential shift

[Jo Jo]

Hello,

I would like to run the BK3 water model on gromacs.  I am using a table to
run this model due to the gaussian charges and buckingham potentials, with
group cutoff scheme.  I think I need to use the 'Potential-shift'
coulomb-modifier to prevent some artificial forces due to discontinuity at
the cutoff, however using coulomb potential shift results in energy
minimization not converging.  With 'Potential-shift-verlet', which is
'None' for group cutoff schemes, no energy minimization issues occur.  I
would appreciate some advice on whether I need 'potential-shift' for the
coulomb interaction, and how this affects the energy minimization.  Below
is my mdp file

On a separate note, I am not sure what to set my rlist, the cutoff distance
of the short-range neighbor list.  Since I am using the group cutoff
scheme, I need to set this value manually.  This should be a cutoff larger
than my coulombic cutoff?

Would appreciate any input on these questions!

Best,

Jo

; RUN CONTROL PARAMETERS
integrator               = md
; Start time and timestep in ps
tinit                    = 0
dt                       = 0.0005
nsteps                   = 1000000
; For exact run continuation or redoing part of a run
init-step                = 0
; Part index is updated automatically on checkpointing (keeps files
separate)
simulation-part          = 1
; mode for center of mass motion removal
comm-mode                = Linear
; number of steps for center of mass motion removal
nstcomm                  = 50
; group(s) for center of mass motion removal
comm-grps                = System

; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol                    = 1.0
emstep                   = 0.01
; Max number of iterations in relax-shells
niter                    = 100
; Step size (ps^2) for minimization of flexible constraints
fcstep                   = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep               = 1000
nbfgscorr                = 10

; OUTPUT CONTROL OPTIONS
; Output frequency for energies to log file and energy file
nstlog                   = 1000
nstcalcenergy            = 50
nstenergy                = 1000
; Output frequency and precision for .xtc file
nstxout-compressed       = 100
compressed-x-precision   = 1000
; This selects the subset of atoms for the compressed
; trajectory file. You can select multiple groups. By
; default, all atoms will be written.
compressed-x-grps        =
; Selection of energy groups
energygrps               = OW GM GH

; NEIGHBORSEARCHING PARAMETERS
; cut-off scheme (Verlet: particle based cut-offs, group: using charge
groups)
cutoff-scheme            = group ;Verlet
; nblist update frequency
nstlist                  = 20
; ns algorithm (simple or grid)
ns_type                  = grid
; Periodic boundary conditions: xyz, no, xy
pbc                      = xyz
periodic-molecules       = no
; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,
; a value of -1 means: use rlist
verlet-buffer-tolerance  = 0.005
; nblist cut-off
rlist                    = 1.0
; long-range cut-off for switched potentials
;rlistlong                = -1
;nstcalclr                = -1

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = PME-user
coulomb-modifier         = Potential-shift ;Potential-shift-Verlet
rcoulomb-switch          = 0
rcoulomb                 = 0.9
; Relative dielectric constant for the medium and the reaction field
epsilon-r                = 1
epsilon-rf               = 0
; Method for doing Van der Waals
vdw-type                 = user
vdw-modifier             = ;Potential-shift-Verlet
; cut-off lengths
rvdw-switch              = 0
rvdw                     = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension          = 1
; Separate tables between energy group pairs
energygrp-table          = OW OW GM GM GM GH GH GH

; 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-06
ewald-rtol-lj            = 0.001
lj-pme-comb-rule         = Geometric
ewald_geometry           = 3d
epsilon_surface          = 0

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl                   = nose-hoover
nsttcouple               = -1
nh-chain-length          = 1
print-nose-hoover-chain-variables = no
; Groups to couple separately
tc-grps                  = System
; Time constant (ps) and reference temperature (K)
tau_t                    = 1.0
ref_t                    = 298.15
; pressure coupling
Pcoupl                   = berendsen ;Parrinello-Rahman
pcoupltype               = Isotropic
nstpcouple               = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p                    = 2.0
compressibility          = 4.5e-5
ref_p                    = 100.0
; Scaling of reference coordinates, No, All or COM
refcoord-scaling         = all

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel                  = no
gen_temp                 = 298.15
gen_seed                 = -1

; OPTIONS FOR BONDS
constraints              = none
; Type of constraint algorithm
constraint-algorithm     = Lincs
; Do not constrain the start configuration
continuation             = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR                = no
; Relative tolerance of shake
shake-tol                = 0.0001
; Highest order in the expansion of the constraint coupling matrix
lincs-order              = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter               = 1
; 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