VMD-L Mailing List

From: Justin Gullingsrud (justinrocks_at_gmail.com)
Date: Tue Aug 10 2004 - 13:31:01 CDT

Hi,

Yes, if you modify a molecule's coordinates and then write out a
trajectory file, it will reflect changes to those coordinates. In
batch mode, you can enter:

  mol load psf somefile.psf dcd somefile.dcd
  # --
  # -- modify coordinates, align frames, etc.
  # --
  animate write dcd newfile.dcd waitfor all
  exit

The "waitfor all" ensures that all frames get written before VMD exits.

In batch mode, there's another trick you can do. Say you start VMD
with the following command line arguments:

  vmd -dispdev text -e analysis.tcl -args file1.dcd file2.dcd

The "-args" option causes everything that comes after it to be
combined into a Tcl variable called argv, which could be accessed from
your analysis.tcl script like so:

  set f1 [lindex $argv 0]
  set f2 [lindex $argv 1]

This can make it easier to reuse analysis scripts since you don't have
to hardcode the name of the files you want to process.

Cheers,
Justin

On Tue, 10 Aug 2004 09:46:12 -0700 (PDT), Vani Krishna
<vakri2002_at_yahoo.com> wrote:
> Hi:
>
> if i need to change something in each frame and write
> back a new dcd in batch mode, how do i do that?
>
> will 'writepdb'/'writedcd' work in this case? how do i
> tell VMD to write a new dcd after reading in an old
> one? (in batch mode, i don't want to open VMD console)
>
> Thanks
>
>
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