[gmx-users] temperature coupling groups for homogeneous mixtures/ ionic liquids?

[Kroon, P.C.]

Hi,

yes it matters. In general tc-grps=system is better/correct, unless the
thermal energy transfer across your system is hampered (e.g. a lipid
membrane, or a large protein). It hasn't changed with versions. In
addition, the Berendsen thermostat produces the wrong ensemble.
To check previous simulations, check that the system as a whole, as well as
relevant parts of your simulations display the correct maxwell-boltzmann
distribution of velocities. Even then, there might be some effect which are
hard to quantify.

Peter

On Mon, Jan 16, 2017 at 8:12 PM, Boning Wu <bw194 at scarletmail.rutgers.edu>
wrote:

> Dear Gromacs Users,
>
> I am simulating ionic liquids and the mixtures of ionic liquids and neutral
> solvents. I used Berendsen or Nose-Hoover temperature coupling for NPT
> systems. No constrains or restrains are in the system.
>
> I just find these discussions and documentations about the temperature
> coupling groups:
>
> http://www.mail-archive.com/gmx-users@gromacs.org/msg28634.html
>
> http://www.gromacs.org/Documentation/Terminology/Thermostats
>
> I am worried because without realizing the limitations of temperature
> coupling, I used to set my tc groups very arbitrarily in my previous
> simulations, sometimes I use
>
> tc-grps             =  CATION ANION NEUTRAL
> and sometimes I use:
>
> tc-grps             =  system
>
> Here are my questions:
>
> 1. Of these two grouping methods, which is better for systems
> (a) which is completely homogeneous?
> and (b) which has some nano-domain structures like the aggregations of
> neutral molecules in ionic liquids with size up to 2 nm ( but no phase
> segregation)?
>
> 2. Since now it's almost not possible to re-run all my simulations, does it
> matter if I use two methods arbitrarily? I have attached an mdp file. Most
> work is done by 5.0.4 and 2016.1. How could I check if there is artifact in
> my system?
>
> 3. Since most of the discussions I found are several years ago, did things
> get improved these years? For example, is there anything improved after
> cut-off scheme is replaced by Verlet?
>
> Any help would be appreciated!
>
> Here is my .mdp file
>
> title               =  productrun
> cpp                 =  /lib/cpp
> define              =
> constraints         =  none
> integrator          =  md
> dt                  =  0.001    ; ps !
> nsteps              =  2000000  ; 2 ns
> nstcomm             =  1
> nstxout             =  500000   ; write x to trr file
> nstvout             =  500000   ; write v to trr file
> nstxtcout           =  1000     ; write x to xtc file
> nstfout             =  0
> nstlog              =  1000     ; write energy to log
> nstenergy           =  1000     ; write energy to edr
> nstlist             =  1        ; frequency to update neighbour list
> ; GPU parameters
> ;verlet-buffer-tolerance  = -1
> ;nstcalclr                =  1
> ;nstcalcenergy            =  1
> ns_type             =  grid
> pbc                 =  xyz      ; periodic boundry condition
> rlist               =  1.5
> rcoulomb            =  1.5
> rvdw                =  1.5
> disre               =  simple
> disre-fc            =  1000
> coulombtype         =  PME
> ; Apply long range dispersion corrections for Energy and Pressure =
> DispCorr            =  EnerPres
> ; Spacing for the PME/PPPM FFT grid =
> fourierspacing      = 0.08  ; depends on system
> ; 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                = 6
> ewald_rtol               = 1e-05
> ewald_geometry           = 3d
> epsilon_surface          = 0
> optimize_fft             = yes
> ; Nose-Hoover temperature coupling is on
> Tcoupl              =  Nose-Hoover
> tc-grps             =  system
> tau_t               =  0.2  ; depending on system
> ref_t               =  298.0
> energygrps          =  system
> ; Pressure coupling is on
> Pcoupl              = Parrinello-Rahman
> Pcoupltype          = isotropic
> tau_p               =  1.0    ; depending on system
> compressibility     =  4.5e-5
> ref_p               =  1.0
> gen_vel             =  no
> gen_temp            =  298.0
> gen_seed  =  43697
>
>
> Thank you,
> Boning Wu
> --
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