[gmx-users] Different temperatures for different groups, even with Nose-Hoover
Justin A. Lemkul
jalemkul at vt.edu
Thu Oct 29 22:38:48 CET 2009
Michael Lerner wrote:
> 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
>
I see you are using "constraints = none," but are there any constraints defined
in the topology? If so, as noted in g_traj -h:
"Option -ot plots the temperature of each group, provided velocities are
present in the trajectory file. No corrections are made for constrained
degrees of freedom! This implies -com."
So you will get an inherently incorrect answer when using g_traj, if there are
any constraints.
-Justin
> 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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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