<br><br><div class="gmail_quote">On Thu, Oct 29, 2009 at 5:38 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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></div>
I see you are using "constraints = none," but are there any constraints defined in the topology? If so, as noted in g_traj -h:<br>
<br>
"Option -ot plots the temperature of each group, provided velocities are<br>
present in the trajectory file. No corrections are made for constrained<br>
degrees of freedom! This implies -com."<br>
<br>
So you will get an inherently incorrect answer when using g_traj, if there are any constraints.<br>
<br></blockquote><div><br>Oops! I actually had read some previous messages about that, but I got confused and thought the problem was with g_energy, not g_traj. I'm not particularly familiar with the GROMACS source code, but gmx_traj.c has this function:<br>
<br>static real temp(rvec v[],real mass[],int isize,atom_id index[])<br>{<br> real ekin2=0;<br> int i,j;<br><br> for(i=0; i<isize; i++) {<br> j = index[i];<br> ekin2 += mass[j]*norm2(v[j]);<br> }<br><br> return ekin2/(3*isize*BOLTZ);<br>
}<br><br>so it looks like g_traj is just assuming that there are 3*N degrees of freedom. My protein topology file has 304 particles and 83 lines in the constraints section, so I think the correction should be <br><br>295.3496*((3*304)/(3*304 - 83)) = 324.9202<br>
<br>for my protein vs. 322.9525 for the W's and 322.9279 for the WF's.<br><br>So, they're still a little off, but doing some block averaging and looking at standard errors, it's well within the acceptable range.<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;">
-Justin<br>
<br>
<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">
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>
<br>
<br></div></div>
------------------------------------------------------------------------<div class="im"><br>
<br>
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</div></blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<div><div></div><div class="h5"><br>
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</div></div></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>