[gmx-users] RE: log files

Nimesh Jain nimeshjain2010 at u.northwestern.edu
Wed Aug 11 16:52:08 CEST 2010


Hi,

I am having some problem in my simulations related to log files. The file
sizes are enormous, its like after 3 days of simulation I had a 20 GB md.log
file. One of my grompps looks like this:
[tau_t is very low because I am using bd and it doesn't work otherwise]. [I
am doing a replica exchange with 10,000 as exchange frequency]


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

nstlog                   = 100000
nstenergy                = 1000

nstxtcout                = 1000
xtc-precision            = 1000

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 P260 SA SB

energygrp_table          = A A  A T  A G  A C  A P260  A SA  A SB  T T  T G
T C  T P260  T S
A  T SB  G G  G C  G P260  G SA  G SB  C C  C P260  C SA  C SB  P260 P260
P260 SA  P260 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                    = 0.0001
ref_t                    = 260.00

Pcoupl                   = No

andersen_seed            = 815131

gen_vel                  = yes
gen_temp                 = 260.0000
gen_seed                 = 1993

; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp_excl           =



Please let me know if anyone knows whats the problem.

Thanks,
Nimesh
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