[gmx-users] RE:How to change the screen's output frequency?
chris.neale at utoronto.ca
chris.neale at utoronto.ca
Mon Oct 3 16:04:33 CEST 2011
Speaking of which, I think that all programs should by default list
-hidden when they are run with -h so that users are aware that there
are hidden options and know how to access them. The -h output could
clearly indicate that such options are not fully tested, etc.
Chris.
Justin A. Lemkul jalemkul at vt.edu
Mon Oct 3 15:56:45 CEST 2011
* Previous message: [gmx-users] RE:How to change the screen's
output frequency?
* Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
?? wrote:
> On 2011-10-02 17:14, ?????? 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
--
More information about the gromacs.org_gmx-users
mailing list