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

[Justin A. Lemkul]

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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