[gmx-users] Brownian Dynamics Simulations generating huge log files

[Justin A. Lemkul]

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>> 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> | (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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================