[gmx-users] setting up a simulation of an ionic liquid
Laura Leay
laura.leay at postgrad.manchester.ac.uk
Mon May 13 17:50:25 CEST 2013
All,
I've seen a few threads about simulations in ionic liquds but have not come across anything that tells me what settings I should use in my mdp file. The system is nitric acid which has fully dissociated into NO3- and HO3+. The simulation will run fine with just the ions at low density under NVT. However, when I solvate the box with SPC water (using the Amber force field) the simulation energy minimises with a really maximum force, of the order of 10^5. If I try to run an NPT simulation it immediately crashes and the md.log fle reveals that the electrostatic potential was unreasonable high, resulting in NaN.
Below is the mdp file I've been using. I've been using PME electrostatics. If anyone can suggest some changes to make I would appreciate it.
Laura
PS, Justin, you were right earlier, there was a problem with my toplogy causing renaming of residues, I just hadn't spotted it. Thanks for your reply.
-------------
; VARIOUS PREPROCESSING OPTIONS
title = Yo
cpp = /usr/bin/cpp
include =
;define = -DFLEXIBLE
; RUN CONTROL PARAMETERS
integrator = steep ;md for simulation, steep for Emin
; Start time and timestep in ps
tinit = 0
dt = 0.0001
nsteps = 50000000 ;remove 3
; For exact run continuation or redoing part of a run
init_step = 0
; 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 = 300
bd-fric = 0
ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 100
emstep = 0.01
; Max number of iterations in relax_shells
niter = 20
; Step size (1/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 coords (x), velocities (v) and forces (f)
nstxout = 0
nstvout = 0
nstfout = 0
; Checkpointing helps you continue after crashes
nstcheckpoint = 1000
; Output frequency for energies to log file and energy file
nstlog = 50
nstenergy = 50
; Output frequency and precision for xtc file
nstxtcout = 50
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 (default), no (vacuum)
; or full (infinite systems only)
pbc = xyz
; nblist cut-off
rlist = 0.9
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 0.9
; 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 = 1.5
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; 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
; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 2
; Salt concentration in M for Generalized Born models
gb_saltconc = 0
; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
implicit_solvent = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = berendsen
; Groups to couple separately
tc-grps = System
; Time constant (ps) and reference temperature (K)
tau_t = 0.1
ref_t = 300
; Pressure coupling
Pcoupl = berendsen
Pcoupltype = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 1.0
compressibility = 0 4.5e-5
ref_p = 1.0 1.0
; Random seed for Andersen thermostat
andersen_seed = 815131
; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing = no
; Number of time points to use for specifying annealing in each group
annealing_npoints =
; List of times at the annealing points for each group
annealing_time =
; Temp. at each annealing point, for each group.
annealing_temp =
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen_temp = 300
gen_seed = 1993
; OPTIONS FOR BONDS
;constraints = all-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
; 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
; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp_excl =
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