[gmx-users] bk3 water energy minimization potential shift
Jo Jo
jojo4122202 at gmail.com
Fri Aug 31 17:59:49 CEST 2018
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
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