[gmx-users] Brownian Dynamics Simulations generating huge log files
Justin A. Lemkul
jalemkul at vt.edu
Thu Dec 16 21:09:37 CET 2010
Nimesh Jain wrote:
> I am attaching the file, The simulation doesn't seem to crash, the log
> gets updated for sure. Hope you can make some sense of it.
>
A few things:
1. Please do not attach entire log files. That took forever for my mail client
to download with no ability to abort.
http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette
2. Since I had already downloaded such an enormous file, I looked through it
anyway, and found several potential problems:
a. You probably have problems in your tables:
"WARNING: For the 4981 non-zero entries for table 2 in table_SA_SB.xvg the
forces deviate on average 44% from minus the numerical derivative of the potential"
b. Your value of nstlog is nonsense: "nstlog = 1215752192" indicates that mdrun
did not find a reasonable value, i.e. you have exceeded the maximum size for an
integer. Use a large, but sensible, setting.
c. Your system is exploding, with a temperature of 1.14469e+04.
I suspect that the large log file is produced by the instability of the system,
and hence you're getting a huge amount of diagnostic information, much of which
is somewhat cryptic.
-Justin
> On Thu, Dec 16, 2010 at 1:50 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Nimesh Jain wrote:
>
> I set nstlog = 100000000000, and still I get a 5MB log file
> within a minute of starting the sim. It seems absurd, but its
> happening :(
>
>
> Well, a log file will always be written with header information,
> etc, although 5 MB does seem quite large. The better question is
> whether or not it continues to get updated, causing the file size to
> increase. If it is, investigate what the contents are. Is the
> simulation crashing, causing thousands of lines of LINCS warnings to
> be printed? Is it normal output, but at a different frequency than
> what was specified?
>
> -Justin
>
> On Thu, Dec 16, 2010 at 10:05 AM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> Nimesh Jain wrote:
>
> Hi,
>
> I am trying to simulate a system of 880 particles with
> implicit
> solvent using brownian dynamics, but the simulation generates
> huge log files (it writes md.log files at a rate of almost
> 5MB/minute) and this crashed my system since I ran out of
> space :(
>
> My mdp file looks like this:
>
> include =
> define =
> integrator = bd
> tinit = 0
> dt = 0.001
> nsteps = 100000000 ;100000
> simulation_part = 1
> init_step = 0
> comm-mode = Angular
> nstcomm = 1
> comm-grps =
>
> emtol = 0.01
> emstep = 1.5
>
> nstxout = 10000
> nstvout = 10000
> nstfout = 10000
>
> nstenergy = 1000
>
> nstxtcout = 1000
> xtc-precision = 1000
>
> nstlog = 0
>
> xtc-grps =
> energygrps =
>
> ns_type = grid
> pbc = xyz
> periodic_molecules = no
>
> rlist = 8.95
>
> coulombtype = user
> rcoulomb-switch = 0
> rcoulomb = 8.95
> epsilon-r = 1
>
> vdw-type = user ;cutoff
> rvdw-switch = 0
> rvdw = 8.95
> DispCorr = No
> table-extension = 1
>
> ; Seperate tables between energy group pairs
> energygrps = A T G C P300 SA SB
>
>
> energygrp_table = A A A T A G A C A P300 A
> SA A
> SB T T T G T C T P300 T SA T SB G G G C G P300
> G SA G
> SB C C C P300 C SA C SB P300 P300 P
> 300 SA P300 SB SA SA SA SB SB SB
>
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing = 0.10
>
> Tcoupl = Nose-Hoover
> tc-grps = System
> tau_t = 0.001
>
>
> This doesn't seem like a reasonable setting for tau_t; grompp
> should
> have warned you about that since dt = tau_t!
>
>
> ref_t = 300.00
>
> Pcoupl = No
>
> andersen_seed = 815131
>
> gen_vel = yes
> gen_temp = 300.0000
> gen_seed = 1993
>
> Please let me know if there is a solution to write
> smaller mdp
> files. I have set nstlog = 0 , but even that doesn't work!
>
>
> Set nstlog to some incredibly large number, then, and it will
> only
> output a few times. It seems strange that nstlog = 0 didn't
> suppress the .log file output as it would any of the other nst*
> settings.
>
> -Justin
>
>
> Thanks
> Nimesh
>
>
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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>
> --
> Nimesh Jain
> Graduate Student
> Biomedical Engineering
> Northwestern University
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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