[gmx-users] RE:How to change the screen's output frequency?

[Justin A. Lemkul]

杜波 wrote:
> On 2011-10-02 17:14, 杜波 wrote:
>> How to change the screen's output frequency?
>>
>> ol 0.85  imb F  6% step 4188000, remaining runtime:   174 s
>> vol 0.87  imb F  3% step 4188100, remaining runtime:   174 s
>> vol 0.86  imb F  1% step 4188200, remaining runtime:   174 s
>> vol 0.86  imb F  4% step 4188300, remaining runtime:   174 s
>> vol 0.88  imb F  6% step 4188400, remaining runtime:   174 s
>> vol 0.87  imb F  3% step 4188500, remaining runtime:   174 s
>> vol 0.88  imb F  8% step 4188600, remaining runtime:   174 s
>> vol 0.88  imb F  6% step 4188700, remaining runtime:   174 s
>> vol 0.86  imb F  3% step 4188800, remaining runtime:   174 s
>> vol 0.87  imb F  4% step 4188900, remaining runtime:   174 s
>> vol 0.86  imb F  1% step 4189000, remaining runtime:   174 s
>> vol 0.86  imb F  5% step 4189100, remaining runtime:   174 s
>> vol 0.87  imb F  4% step 4189200, remaining runtime:   173 s
>> vol 0.88  imb F  6% step 4189300, remaining runtime:   173 s
>> vol 0.85  imb F  1% step 4189400, remaining
>>
> mdrun -h
> 
> I have done that ,but i did not fing the option!
> 

The option is hidden, try mdrun -h -hidden.  You can use the -stepout option to 
set the output frequency.  Or, you can turn off -v altogether.

-Justin

> The following are the  mdrun's  options .
> 
> 
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -s      topol.tpr  Input        Run input file: tpr tpb tpa
>   -o       traj.trr  Output       Full precision trajectory: trr trj cpt
>   -x       traj.xtc  Output, Opt. Compressed trajectory (portable xdr format)
> -cpi      state.cpt  Input, Opt.  Checkpoint file
> -cpo      state.cpt  Output, Opt. Checkpoint file
>   -c    confout.gro  Output       Structure file: gro g96 pdb etc.
>   -e       ener.edr  Output       Energy file
>   -g         md.log  Output       Log file
> -dhdl      dhdl.xvg  Output, Opt. xvgr/xmgr file
> -field    field.xvg  Output, Opt. xvgr/xmgr file
> -table    table.xvg  Input, Opt.  xvgr/xmgr file
> -tablep  tablep.xvg  Input, Opt.  xvgr/xmgr file
> -tableb   table.xvg  Input, Opt.  xvgr/xmgr file
> -rerun    rerun.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
> -tpi        tpi.xvg  Output, Opt. xvgr/xmgr file
> -tpid   tpidist.xvg  Output, Opt. xvgr/xmgr file
>  -ei        sam.edi  Input, Opt.  ED sampling input
>  -eo        sam.edo  Output, Opt. ED sampling output
>   -j       wham.gct  Input, Opt.  General coupling stuff
>  -jo        bam.gct  Output, Opt. General coupling stuff
> -ffout      gct.xvg  Output, Opt. xvgr/xmgr file
> -devout   deviatie.xvg  Output, Opt. xvgr/xmgr file
> -runav  runaver.xvg  Output, Opt. xvgr/xmgr file
>  -px      pullx.xvg  Output, Opt. xvgr/xmgr file
>  -pf      pullf.xvg  Output, Opt. xvgr/xmgr file
> -mtx         nm.mtx  Output, Opt. Hessian matrix
>  -dn     dipole.ndx  Output, Opt. Index file
> 
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   yes     Print help info and quit
> -[no]version bool   no      Print version info and quit
> -nice        int    0       Set the nicelevel
> -deffnm      string         Set the default filename for all file options
> -xvg         enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
> -[no]pd      bool   no      Use particle decompostion
> -dd          vector 0 0 0   Domain decomposition grid, 0 is optimize
> -npme        int    -1      Number of separate nodes to be used for PME, -1
>                             is guess
> -ddorder     enum   interleave  DD node order: interleave, pp_pme or cartesian
> -[no]ddcheck bool   yes     Check for all bonded interactions with DD
> -rdd         real   0       The maximum distance for bonded interactions with
>                             DD (nm), 0 is determine from initial coordinates
> -rcon        real   0       Maximum distance for P-LINCS (nm), 0 is estimate
> -dlb         enum   auto    Dynamic load balancing (with DD): auto, no or yes
> -dds         real   0.8     Minimum allowed dlb scaling of the DD cell size
> -gcom        int    -1      Global communication frequency
> -[no]v       bool   no      Be loud and noisy
> -[no]compact bool   yes     Write a compact log file
> -[no]seppot  bool   no      Write separate V and dVdl terms for each
>                             interaction type and node to the log file(s)
> -pforce      real   -1      Print all forces larger than this (kJ/mol nm)
> -[no]reprod  bool   no      Try to avoid optimizations that affect binary
>                             reproducibility
> -cpt         real   15      Checkpoint interval (minutes)
> -[no]cpnum   bool   no      Keep and number checkpoint files
> -[no]append  bool   yes     Append to previous output files when continuing
>                             from checkpoint instead of adding the simulation
>                             part number to all file names
> -maxh        real   -1      Terminate after 0.99 times this time (hours)
> -multi       int    0       Do multiple simulations in parallel
> -replex      int    0       Attempt replica exchange every # steps
> -reseed      int    -1      Seed for replica exchange, -1 is generate a seed
> -[no]ionize  bool   no      Do a simulation including the effect of an X-Ray
>                             bombardment on your system
> 
> 
> thanks!!
>> Bo Du
>> Department of Polymer Science and Engineering,
>> School of Chemical Engineering and technology,
>> Tianjin University, Weijin Road 92, Nankai District 300072,
>> Tianjin City P. R. China
>> Tel/Fax: +86-22-27404303
>> E-mail: 2008dubo at gmail.com

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

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

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