[gmx-users] RE: log files

[Gaurav Goel]

On Wed, Aug 11, 2010 at 1:10 PM, Nimesh Jain <
nimeshjain2010 at u.northwestern.edu> wrote:

> 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.
>
> Did you re-compile using grompp after changing nstlog? Otherwise in md.tpr
(output of grompp), nstlog=1000.

-Gaurav

>
> 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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