[gmx-users] RE: log files

[Justin A. Lemkul]

Nimesh Jain 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.
> 

Then look at what it's writing.  Is it giving the output you expect?  Are all 
replicas written to the same log file?  I haven't used REMD since Gromacs 3.x, 
when replicas were written to separate logs, I don't know if it's changed.  I'd 
be far more concerned with outputting full precision coordinates and velocities 
every 10 ps - that will likely occupy huge amounts of disk space.

And as an aside, when you directly say a certain .mdp file produces a 20 GB log 
file, the users of this list will expect that to be accurate.  If you're not 
telling the whole truth, then it makes it hard to diagnose any issues and 
discourages people from helping you.  Accurate reporting makes for faster 
resolution.

-Justin

> On Wed, Aug 11, 2010 at 10:49 AM, Gaurav Goel <gauravgoeluta at gmail.com 
> <mailto: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
>     <mailto: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
> 
>         --
>         gmx-users mailing list    gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>         http://lists.gromacs.org/mailman/listinfo/gmx-users
>         Please search the archive at http://www.gromacs.org/search
>         before posting!
>         Please don't post (un)subscribe requests to the list. Use the
>         www interface or send it to gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>.
>         Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 
>     --
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at http://www.gromacs.org/search before
>     posting!
>     Please don't post (un)subscribe requests to the list. Use the
>     www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 
> 
> -- 
> Nimesh Jain
> Graduate Student
> Biomedical Engineering
> Northwestern University
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================