[gmx-users] Different temperatures for different groups, even with Nose-Hoover

[Michael Lerner]

Hi,

I'm using GROMACS 4.0.5 to do a MARTINI simulation of a CG protein in a CG
water box, looking at the diffusion constant of the protein among other
things. I'm using the Nose-Hoover thermostat and Parrinello-Rahman barostat
with tc-grps = System. In CHARMM, a protein-in-water simulation with an
extended ensemble will show equal temperatures for the protein and the
water. However, I'm finding that, with ref_t = 323, I get a SOL (both W and
WF particles) temperature of 323 and a Protein temperature of 295. Is this
what I should expect?

The system has 62.5k particles, the box is 20 x 20 x 20, and the relevant
.mdp parameters I've used are:

tcoupl                   = Nose-Hoover
tc-grps                  = System
tau_t                    = 2
ref_t                    = 323
Pcoupl                   = Parrinello-Rahman
Pcoupltype               = isotropic
tau_p                    = 5
compressibility          = 5e-5
ref_p                    = 1.0

These parameters seem to lead to stable systems for bilayer simulations.
I've included the whole .mdp file at the end in case I've forgotten to
mention something relevant.

I calculated temperatures with

g_traj -f md2.trr -s md2.tpr -n index.ndx -ot -ng 5

Thanks,

-Michael

------ begin md2.mdp ------

; RUN CONTROL PARAMETERS =
integrator               = md
; start time and timestep in ps =
tinit                    = 0.0
dt                       = 0.020
nsteps                   = 25500000
; 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                = System


; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout                  = 50000
nstvout                  = 50000
nstfout                  = 0
; Output frequency for energies to log file and energy file =
nstlog                   = 2500
nstenergy                = 2500
; Output frequency and precision for xtc file =
nstxtcout                = 2500
xtc_precision            = 100
; 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               = System Protein W WF

; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist                  = 5
; ns algorithm (simple or grid) =
ns_type                  = grid
; Periodic boundary conditions: xyz or none =
pbc                      = xyz
; nblist cut-off         =
rlist                    = 1.2

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype              = Shift
rcoulomb_switch          = 0.0
rcoulomb                 = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r                = 15
; Method for doing Van der Waals =
vdw_type                 = Shift
; cut-off lengths        =
rvdw_switch              = 0.9
rvdw                     = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr                 = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing           = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx               = 10
fourier_ny               = 10
fourier_nz               = 10
; EWALD/PME/PPPM parameters =
pme_order                = 4
ewald_rtol               = 1e-05
epsilon_surface          = 0
optimize_fft             = no

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
tcoupl                   = Nose-Hoover
; Groups to couple separately =
tc-grps                  = System
; Time constant (ps) and reference temperature (K) =
tau_t                    = 2
ref_t                    = 323
; Pressure coupling      =
Pcoupl                   = Parrinello-Rahman
Pcoupltype               = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p                    = 5
compressibility          = 5e-5
ref_p                    = 1.0

; SIMULATED ANNEALING CONTROL =
annealing                = no

; GENERATE VELOCITIES FOR STARTUP RUN =
continuation      = yes
gen_vel                  = no
;gen_temp                 = 323
;gen_seed                 = 473529

; OPTIONS FOR BONDS     =
constraints              = none
; Type of constraint algorithm =
constraint_algorithm     = Lincs
; Relative tolerance of shake =
shake_tol                = 0.0001
; Highest order in the expansion of the constraint coupling matrix =
lincs_order              = 4
; 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

; NMR refinement stuff  =
; Distance restraints type: No, Simple or Ensemble =
disre                    = No
; Force weighting of pairs in one distance restraint: Equal or Conservative
=
disre_weighting          = Equal
; Use sqrt of the time averaged times the instantaneous violation =
disre_mixed              = no
disre_fc                 = 1000
disre_tau                = 1.25
; Output frequency for pair distances to energy file =
nstdisreout              = 100
------- end md2.mdp -------



-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
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