[gmx-users] why the trajectory file is not output
He, Yang
yang.he at mavs.uta.edu
Fri Jan 23 21:38:02 CET 2009
I just tried it several times and still can not get the trajectory file. I am using the 3.3.1 not new version but I can get the xtc or trr file when running the other cases .
Yang
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
Sent: Friday, January 23, 2009 12:09 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] why the trajectory file is not output
He, Yang wrote:
> yes, I mean that when using the command "mdrun", the traj.xtc file is not ouput at all while the other files like "topol.tpr, ener.edr,md.log, mdout.mdp" are all output.
>
Well, neither topol.tpr nor mdout.mdp are produced by mdrun (they are produced
by grompp), so that doesn't suggest anything important.
There are several questions that might provide some useful information:
1. Do md.log or ener.edr continue to get written to?
2. Is a .trr ever produced? Its absence leads me to believe that you are simply
not being patient :) As I said before, data is buffered and not continually output.
3. What version of Gromacs are you using? Are you running in parallel, and if
so, do other MPI codes work on the same box/cluster?
-Justin
> Hence, I just got confused about that.
>
> Yang
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
> Sent: Friday, January 23, 2009 11:55 AM
> To: Gromacs Users' List
> Subject: Re: [gmx-users] why the trajectory file is not output
>
> He, Yang wrote:
>> I think this problem is not due to the disk space cause I check that it has a large space in the fold. I have tried some times but always the same results ,no trajectory files while the others are normal .
>>
>
> What files are produced? And again, are you referring to the absence of the
> trajectory *during* the simulation, or after? Which trajectory, .trr or .xtc,
> is missing?
>
> -Justin
>
>> Thank you very much for your reply.
>>
>> Yang
>> ________________________________________
>> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
>> Sent: Friday, January 23, 2009 11:42 AM
>> To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] why the trajectory file is not output
>>
>> He, Yang wrote:
>>> Hi all the users,
>>>
>>> When I use the command "mdrun"to simulate the CG DNA model, I found that all the files are output expect the trajectory file. I will list some parts of my mdp.file
>>>
>> During the simulation? Data is buffered, so you may not see immediate output.
>> Or is the trajectory absent at the end of the simulation? That might indicate a
>> problem with available disk space, depending on how large the file is.
>>
>> -Justin
>>
>>> ; RUN CONTROL PARAMETERS =
>>> integrator = md
>>> ; start time and timestep in ps =
>>> tinit = 0.0
>>> dt = 0.03
>>> nsteps = 1000000
>>> ; number of steps for center of mass motion removal =
>>> nstcomm = 1
>>>
>>>
>>> ; OUTPUT CONTROL OPTIONS =
>>> ; Output frequency for coords (x), velocities (v) and forces (f) =
>>> nstxout = 5000
>>> nstvout = 5000
>>> nstfout = 0
>>> ; Output frequency for energies to log file and energy file =
>>> nstlog = 1000
>>> nstenergy = 1000
>>> ; Output frequency and precision for xtc file =
>>> nstxtcout = 1000
>>> xtc_precision = 1000
>>> ; 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 = plan1 NA CL W
>>>
>>> ; NEIGHBORSEARCHING PARAMETERS =
>>> ; nblist update frequency =
>>> nstlist = 10
>>> ; ns algorithm (simple or grid) =
>>> ns_type = grid
>>> ; Periodic boundary conditions: xyz or none =
>>> pbc = xyz
>>> ; nblist cut-off =
>>> rlist = 1.2
>>> domain-decomposition = no
>>>
>>> ; OPTIONS FOR ELECTROSTATICS AND VDW =
>>> ; Method for doing electrostatics =
>>> coulombtype = PME
>>> rcoulomb_switch = 0.0
>>> rcoulomb = 1.2
>>> ; Dielectric constant (DC) for cut-off or DC of reaction field =
>>> epsilon_r = 20
>>> ; Method for doing Van der Waals =
>>> vdw_type = Shift
>>> ; cut-off lengths =
>>> rvdw_switch = 0.9
>>> rvdw = 1.15
>>> ; Apply long range dispersion corrections for Energy and Pressure =
>>> DispCorr = No
>>> ; Spacing for the PME/PPPM FFT grid =
>>> fourierspacing = 0.3
>>> ; FFT grid size, when a value is 0 fourierspacing will be used =
>>> fourier_nx = 0
>>> fourier_ny = 0
>>> fourier_nz = 0
>>> ; EWALD/PME/PPPM parameters =
>>> pme_order = 4
>>> ewald_rtol = 1e-05
>>> epsilon_surface = 0
>>> optimize_fft = yes
>>>
>>> ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
>>> ; Temperature coupling =
>>> tcoupl = Berendsen
>>> ; Groups to couple separately =
>>> tc-grps = plan1 NA CL W
>>> ; Time constant (ps) and reference temperature (K) =
>>> tau_t = 1.0 1.0 1.0 1.0
>>> ref_t = 300 300 300 300
>>> ; Pressure coupling =
>>> Pcoupl = no
>>> Pcoupltype = Isotropic
>>> ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
>>> tau_p = 1.0
>>> compressibility = 1e-5
>>> ref_p = 1.0
>>>
>>>
>>> ; SIMULATED ANNEALING CONTROL =
>>> annealing = no
>>> ; Time at which temperature should be zero (ps) =
>>> zero_temp_time = 0
>>>
>>> ; GENERATE VELOCITIES FOR STARTUP RUN =
>>> gen_vel = yes
>>> gen_temp = 300
>>> gen_seed = 473529
>>>
>>> ; OPTIONS FOR BONDS =
>>> constraints = none
>>> ; Type of constraint algorithm =
>>> constraint_algorithm = Lincs
>>> ; Do not constrain the start configuration =
>>> unconstrained_start = no
>>> ; 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
>>>
>>> ; Free energy control stuff =
>>> free_energy = no
>>> init_lambda = 0
>>> delta_lambda = 0
>>> sc-alpha = 0
>>> sc-sigma = 0.3
>>>
>>> ; Non-equilibrium MD stuff =
>>> acc-grps =
>>> accelerate =
>>> freezegrps =
>>> freezedim =
>>> cos-acceleration =
>>> energygrp_excl =
>>>
>>> ; Electric fields =
>>> ; Format is number of terms (int) and for all terms an amplitude (real) =
>>> ; and a phase angle (real) =
>>> E-x =
>>> E-xt =
>>> E-y = 1 0.05 0.0
>>> E-yt =
>>> E-z =
>>> E-zt =
>>>
>>> ; User defined thingies =
>>> user1-grps =
>>> user2-grps =
>>> userint1 = 0
>>> userint2 = 0
>>> userint3 = 0
>>> userint4 = 0
>>> userreal1 = 0
>>> userreal2 = 0
>>> userreal3 = 0
>>> userreal4 = 0
>>>
>>> Any suggestions will be highly appreciated .
>>>
>>> Thank you very much.
>>>
>>> Yang
>>> _______________________________________________
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>>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> 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://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
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>> 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
> Graduate Research Assistant
> 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://www.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
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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