[gmx-users] RE: log files

[Nimesh Jain]

Well, no. I got a 20GB log file when nstlog was 1000. When I changed it to
10000, the log file was about 1 MB after a few minutes of simulation which
means that it will be in GBs in a few days.

On Wed, Aug 11, 2010 at 10:49 AM, Gaurav Goel <gauravgoeluta at gmail.com>wrote:

> 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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>
>
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-- 
Nimesh Jain
Graduate Student
Biomedical Engineering
Northwestern University
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