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

TJ Piggot t.piggot at bristol.ac.uk
Fri Oct 30 02:29:27 CET 2009


To get g_energy to give you the temperature (or any other property) of a 
specific group you need to have defined appropriate energygrps in your mdp 
file. This is independent of the choice of groups you use for the 
temperature coupling.

If you want to calculate these temperatures of the groups after you have 
already ran your simulations you can use the mdrun -rerun option to save 
you a lot of time.

Tom

--On Thursday, October 29, 2009 18:11:53 -0400 Michael Lerner 
<mglerner+gromacs at gmail.com> 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)



----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.




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