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

[Nimesh Jain]

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 :(

On Thu, Dec 16, 2010 at 10:05 AM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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