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

[Nimesh Jain]

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
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!

Thanks
Nimesh
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