Hi,
If you want to write out an Amber restart file, you need to either
provide the recognized extension for the output trajectory filename
(.rst7) or specify the 'restart' keyword to 'trajout', e.g.
trajout myrestart.rst7
or
trajout myrestart restart
Double check that you're writing the correct format in the output
cpptraj provides. As long as your input trajectory contains velocity
information (because e.g. you are using a NetCDF trajectory with
coordinates + velocities, you've provided a separate velocity
trajectory with the 'mdvel' keyword, etc) your output restart files
will also contain velocity information.
Hope this helps,
-Dan
On Sat, Apr 13, 2019 at 5:41 AM Yuliana Bosken <ydavi002.ucr.edu> wrote:
>
> Hi,
> I have a trajectory 20000 steps (2fs ts for a total of 20 ns) containing
> velocities. I want to save for example every 1000th step as rst file so I
> can restart separate MD runs from each. I tried ptraj input file which
> seems to only allow to convert to dcd and pdb, but the pdb I generated
> contains all frames and I need the 20 separate rst files:
> Here are the options available and part of the script:
> INPUTFILENAME=(
> "md01.mdcrd"
> )
> OUTPUTFILENAME="frame.pdb"
> OUTPUTFORMAT="pdb"
> PRMTOPFILENAME="../02.add_water/water.prmtop"
> # velocity
> VELOCITY="1"
> # nobox
> NOBOX="0"
> # ADVANCED=1 to turn on selection, =0 to turn off
> ADVANCED="1"
> START="1"
> FINAL="50000000"
> FREQ="1000"
> # UNWRAP=1 to unwrap
> UNWRAP="0"
> RESIDUE="1-269"
> CENTER="1-269"
> # STRIPWATER=1 to strip water
> STRIPWATER="0"
> STRIPWATER_FLAG="WAT"
> STRIPION1="0"
> STRIPION1_FLAG="Cl-"
> STRIPION2="0"
> STRIPION2_FLAG="Na+"
> .....
> if [ $OUTPUTFORMAT = "dcd" ]; then
> format="charmm"
> elif [ $OUTPUTFORMAT = "mdcrd" ]; then
> format="trajectory"
> elif [ $OUTPUTFORMAT = "netcdf" ]; then
> format="netcdf"
> elif [ $OUTPUTFORMAT = "pdb" ]; then
> format="pdb"
> fi
>
> if [ $format = "" ]; then
> echo "Format Not Supported"
> else
> TRAJIN=""
> for ix in ${!INPUTFILENAME[*]}
> do
> TRAJIN="$TRAJIN
> trajin ${INPUTFILENAME[$ix]} $argument"
> done
> echo "$TRAJIN
> trajout $OUTPUTFILENAME $format $NOBOX $VELOCITY $argument3 $argument2" >
> $tempfilename
> cpptraj $PRMTOPFILENAME $tempfilename
> rm $tempfilename
> fi
> Thank you in advance!
> Yuliana
>
> --
> Yuliana Bosken
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu Apr 18 2019 - 11:00:04 PDT
