[lammps-users] visualize results from parallel computing results

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1

Ok, thanks a lot.

ziyuan

2

Hi, Axel

Now I don’t know how to build a .psf file through a .dcd dump file. So I wrote this script: “mol new mywater.dcd type dcd waitfor all”. The error is that could not read mywater.dcd file. In README.txt, it is said the native LAMMPS trajectory file should not be binary. But DCD file is binary. So could you help me to generate the .psf file?

Sorry for keeping on this, but thanks for your patience.

ziyuan

3

Hi, Axel

Now I don't know how to build a .psf file through a .dcd dump file. So I
wrote this script: "mol new mywater.dcd type dcd waitfor all". The error is
that could not read mywater.dcd file. In README.txt, it is said the native
LAMMPS trajectory file should not be binary. But DCD file is binary. So
could you help me to generate the .psf file?

if you use a data file, you can generate it directly from it.

   topo readlammpsdata data.rhodo full
   animate write psf rhodo.psf

you have to replace the "full" with whatever atom style you are using.

the second option is to load the dump file from the serial trajectory,
go back to the first step and then also do:

animate write psf myfile.psf

that should produce a .psf file suitable to go with the dcd.

you have to then do the "mol new" on the .psf file and then
do a "mol addfile" on the dcd file. from here on the VMD
documentation and tutorials should provide you with all further
basic VMD related information.

cheers,
    axel.

4

Hi, Axel

I am able to see the results now according to your suggestion.

Thank you very much.

Cheers!

ziyuan