[gmx-users] Different temperatures for different groups, even with Nose-Hoover
XAvier Periole
x.periole at rug.nl
Fri Oct 30 08:28:19 CET 2009
The comment from Justin and your answer to it were pretty convincing.
I think the problem is solved :)).
Tom is correct to get T with g_energy on a simulation that ran with one
Tcoup, you need to rerun the trajectory (trr) with a tpr in which you
define two Tcoup. This should give you T for each group.
XAvier.
On Oct 29, 2009, at 11:11 PM, Michael Lerner wrote:
>
>
> On Thu, Oct 29, 2009 at 5:31 PM, XAvier Periole <x.periole at rug.nl>
> wrote:
>
> On Oct 29, 2009, at 9:26 PM, Michael Lerner wrote:
>
>
> I calculated temperatures with
>
> g_traj -f md2.trr -s md2.tpr -n index.ndx -ot -ng 5
> I did not know you could get the temperature throught g_traj ... the
> -ot option is the one
> giving you the temperature?
>
>
> Yes.
>
> Do you get the same temperature difference with g_energy? Or may be
> the info is not
> in there? May be you could rerun you trajectory using a new tpr
> where you define two
> different temp coupling groups. And see if you observe the same
> temperature given by
> g_energy.
>
> It's possible that I'm doing something wrong, but I couldn't
> convince g_energy to give me the temperature of different groups
> when I used a single thermostat for the entire system. If I use two
> temperature coupling groups, I get the expected results.
>
> As Justin pointed out, it looks like the error was mine for not
> understanding the details of g_traj. When I manually correct for the
> degrees of freedom, I get temperatures for Protein/Sol that are
> close enough to each other (i.e. within a couple of standard
> deviations).
>
> Thanks,
>
> -Michael
>
>
> 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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>
> --
> 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)
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
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> www interface or send it to gmx-users-request at gromacs.org.
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