[gmx-users] setting up a simulation of an ionic liquid
Laura Leay
laura.leay at postgrad.manchester.ac.uk
Tue May 14 11:13:55 CEST 2013
Thanks for the help Justin,
I've taken a look at the atom with the maximum force using VMD and I can't see anything wrong with it. Its part of a whole molecule and not particularly close to any other molecules either. I suspect I may need to take another look at the force field but want to make sure there is nothing in my mdp file that could be causing problems. I've no experience of simulating ionic liquids and from what I've read it can be quite tricky.
The paper I'm using for the nitric is J Phys Chem B, 2001, 105(45), 11131. Here they use a twin range cut off of 12/15 A. The papers for the other molecules I'll eventually be adding to the simulation use a cut off of 15 A so this seemed the most sensible option. Is there anything else you would suggest?
Any help is greatly appreciated.
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: 13 May 2013 23:05
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] setting up a simulation of an ionic liquid
On 5/13/13 11:50 AM, Laura Leay wrote:
> 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.
>
You should investigate which atom bears the maximum force; that will point to
the source of your problem.
> 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.
>
The force field dictates most of the settings, most notably the cutoff. The
value of rvdw seems wrong, at least.
-Justin
> 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 =
>
>
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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