<br><br><div class="gmail_quote">On Thu, Oct 29, 2009 at 5:31 PM, XAvier Periole <span dir="ltr"><<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
On Oct 29, 2009, at 9:26 PM, Michael Lerner wrote:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
I calculated temperatures with<br>
<br>
g_traj -f md2.trr -s md2.tpr -n index.ndx -ot -ng 5<br>
</blockquote></div>
I did not know you could get the temperature throught g_traj ... the -ot option is the one<br>
giving you the temperature?<br>
<br></blockquote><div><br>Yes.<br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Do you get the same temperature difference with g_energy? Or may be the info is not<br>
in there? May be you could rerun you trajectory using a new tpr where you define two<br>
different temp coupling groups. And see if you observe the same temperature given by<br>
g_energy.<br></blockquote><div><br>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.<br>
<br>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).<br>
<br>Thanks,<br><br>-Michael<br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">
<br>
Thanks,<br>
<br>
-Michael<br>
<br>
------ begin md2.mdp ------<br>
<br>
; RUN CONTROL PARAMETERS =<br>
integrator = md<br>
; start time and timestep in ps =<br>
tinit = 0.0<br>
dt = 0.020<br>
nsteps = 25500000<br>
; mode for center of mass motion removal<br>
comm-mode = linear<br>
; number of steps for center of mass motion removal<br>
nstcomm = 1<br>
; group(s) for center of mass motion removal<br>
comm-grps = System<br>
<br>
<br>
; OUTPUT CONTROL OPTIONS =<br>
; Output frequency for coords (x), velocities (v) and forces (f) =<br>
nstxout = 50000<br>
nstvout = 50000<br>
nstfout = 0<br>
; Output frequency for energies to log file and energy file =<br>
nstlog = 2500<br>
nstenergy = 2500<br>
; Output frequency and precision for xtc file =<br>
nstxtcout = 2500<br>
xtc_precision = 100<br>
; This selects the subset of atoms for the xtc file. You can =<br>
; select multiple groups. By default all atoms will be written. =<br>
xtc-grps =<br>
; Selection of energy groups =<br>
energygrps = System Protein W WF<br>
<br>
; NEIGHBORSEARCHING PARAMETERS =<br>
; nblist update frequency =<br>
nstlist = 5<br>
; ns algorithm (simple or grid) =<br>
ns_type = grid<br>
; Periodic boundary conditions: xyz or none =<br>
pbc = xyz<br>
; nblist cut-off =<br>
rlist = 1.2<br>
<br>
; OPTIONS FOR ELECTROSTATICS AND VDW =<br>
; Method for doing electrostatics =<br>
coulombtype = Shift<br>
rcoulomb_switch = 0.0<br>
rcoulomb = 1.2<br>
; Dielectric constant (DC) for cut-off or DC of reaction field =<br>
epsilon_r = 15<br>
; Method for doing Van der Waals =<br>
vdw_type = Shift<br>
; cut-off lengths =<br>
rvdw_switch = 0.9<br>
rvdw = 1.2<br>
; Apply long range dispersion corrections for Energy and Pressure =<br>
DispCorr = No<br>
; Spacing for the PME/PPPM FFT grid =<br>
fourierspacing = 0.12<br>
; FFT grid size, when a value is 0 fourierspacing will be used =<br>
fourier_nx = 10<br>
fourier_ny = 10<br>
fourier_nz = 10<br>
; EWALD/PME/PPPM parameters =<br>
pme_order = 4<br>
ewald_rtol = 1e-05<br>
epsilon_surface = 0<br>
optimize_fft = no<br>
<br>
; OPTIONS FOR WEAK COUPLING ALGORITHMS =<br>
; Temperature coupling =<br>
tcoupl = Nose-Hoover<br>
; Groups to couple separately =<br>
tc-grps = System<br>
; Time constant (ps) and reference temperature (K) =<br>
tau_t = 2<br>
ref_t = 323<br>
; Pressure coupling =<br>
Pcoupl = Parrinello-Rahman<br>
Pcoupltype = isotropic<br>
; Time constant (ps), compressibility (1/bar) and reference P (bar) =<br>
tau_p = 5<br>
compressibility = 5e-5<br>
ref_p = 1.0<br>
<br>
; SIMULATED ANNEALING CONTROL =<br>
annealing = no<br>
<br>
; GENERATE VELOCITIES FOR STARTUP RUN =<br>
continuation = yes<br>
gen_vel = no<br>
;gen_temp = 323<br>
;gen_seed = 473529<br>
<br>
; OPTIONS FOR BONDS =<br>
constraints = none<br>
; Type of constraint algorithm =<br>
constraint_algorithm = Lincs<br>
; Relative tolerance of shake =<br>
shake_tol = 0.0001<br>
; Highest order in the expansion of the constraint coupling matrix =<br>
lincs_order = 4<br>
; Lincs will write a warning to the stderr if in one step a bond =<br>
; rotates over more degrees than =<br>
lincs_warnangle = 30<br>
; Convert harmonic bonds to morse potentials =<br>
morse = no<br>
<br>
; NMR refinement stuff =<br>
; Distance restraints type: No, Simple or Ensemble =<br>
disre = No<br>
; Force weighting of pairs in one distance restraint: Equal or Conservative =<br>
disre_weighting = Equal<br>
; Use sqrt of the time averaged times the instantaneous violation =<br>
disre_mixed = no<br>
disre_fc = 1000<br>
disre_tau = 1.25<br>
; Output frequency for pair distances to energy file =<br>
nstdisreout = 100<br>
------- end md2.mdp -------<br>
<br>
<br>
<br>
-- <br>
Michael Lerner, Ph.D.<br>
IRTA Postdoctoral Fellow<br>
Laboratory of Computational Biology NIH/NHLBI<br>
5635 Fishers Lane, Room T909, MSC 9314<br>
Rockville, MD 20852 (UPS/FedEx/Reality)<br>
Bethesda MD 20892-9314 (USPS)<br></div></div>
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</blockquote></div><br><br clear="all"><br>-- <br>Michael Lerner, Ph.D.<br>IRTA Postdoctoral Fellow<br>Laboratory of Computational Biology NIH/NHLBI<br>5635 Fishers Lane, Room T909, MSC 9314<br>Rockville, MD 20852 (UPS/FedEx/Reality)<br>
Bethesda MD 20892-9314 (USPS)<br>