Particles velocities in VMD

[Jonathan Watkins]

Hi all,

I have a very simple LJ simulation of particles in a 2D box.

Does anyone have nice way of viewing particle velocities in vmd that are output that are from hoomd. The best I can do is to output hundreds of xml files, one for each snapshot. I then have to import these images one at a time into VMD. This is clearly not a god solution.

1) Is there a better way to do this by a different method?

2) If the multiple xml files method is the only way to output the velocities, does anyone know an easy way to import them into VMD?

Thanks,

Jon

[Joshua Anderson]

The next feature release of hoomd, version 1.1 will include a new binary file format capable of storing velocities in the trajectory dump. That will at least enable you to store such data efficiently. I don't know if VMD's molfile plugin architecture allows plugins to provide velocity per frame, though.
------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan
Phone: 734-647-8244
http://www-personal.umich.edu/~joaander/

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[Jonathan Watkins]

Thanks for the reply. I will have a look at the mol file plugin in more detail.

[Benjamin Trefz]

Hey Jon, 

I used to use a bash script like the one below to read multiple xml files into vmd. 

Not sure if that works for your problem.

Best regards,

    Ben

#!/bin/bash

if ( $1 ); then

        echo "Usage: video.sh <path to snapshots>"

else

        cd $1

        ofile="video.tcl"

        array=(`ls *.xml | sort`)

        length=${#array[*]}

        length=$(($length-1))

        echo "#!/usr/bin/tclsh" > $ofile 

        echo "mol new ${array[0]} type hoomd waitfor all" >> $ofile

        for i in $(seq 1 $length); do

                echo "mol addfile ${array[$i]} type hoomd waitfor all" >> $ofile

        done

        echo "animate" >> $ofile

        vmd -e video.tcl

        rm video.tcl    

fi

[Jonathan Watkins]

Yes that is exactly what I needed. Thank you. You have saved me a lot of time.