[gmx-users] Different temperatures for different groups, even with Nose-Hoover
Michael Lerner
mglerner+gromacs at gmail.com
Thu Oct 29 23:07:05 CET 2009
On Thu, Oct 29, 2009 at 5:38 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
> I see you are using "constraints = none," but are there any constraints
> defined in the topology? If so, as noted in g_traj -h:
>
> "Option -ot plots the temperature of each group, provided velocities are
> present in the trajectory file. No corrections are made for constrained
> degrees of freedom! This implies -com."
>
> So you will get an inherently incorrect answer when using g_traj, if there
> are any constraints.
>
>
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:
static real temp(rvec v[],real mass[],int isize,atom_id index[])
{
real ekin2=0;
int i,j;
for(i=0; i<isize; i++) {
j = index[i];
ekin2 += mass[j]*norm2(v[j]);
}
return ekin2/(3*isize*BOLTZ);
}
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
295.3496*((3*304)/(3*304 - 83)) = 324.9202
for my protein vs. 322.9525 for the W's and 322.9279 for the WF's.
So, they're still a little off, but doing some block averaging and looking
at standard errors, it's well within the acceptable range.
Thanks,
-Michael
> -Justin
>
> 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)
>>
>>
>> ------------------------------------------------------------------------
>>
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
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)
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091029/aa28330f/attachment.html>
More information about the gromacs.org_gmx-users
mailing list