[gmx-users] RE: log files

[Gaurav Goel]

You've set the frequency of writing to log file as 'nstlog
= 100000'.
Given that 'nsteps                   = 100000000', you're writing to the log
file only 1000 times. Do you get a 20GB md.log file with these settings?

-Gaurav

On Wed, Aug 11, 2010 at 10:52 AM, Nimesh Jain <
nimeshjain2010 at u.northwestern.edu> wrote:

> 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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