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
<[email protected]> wrote:
On Thu, Oct 29, 2009 at 5:31 PM, XAvier Periole <[email protected]> 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
[email protected]
University of Bristol, UK.
_______________________________________________
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