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

Michael Lerner mglerner+gromacs at gmail.com
Thu Oct 29 23:11:53 CET 2009


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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>
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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)
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