From: Adam Goler (
Date: Tue Mar 18 2014 - 09:09:38 CDT

Hi Ramin,

I personally found this much simpler to do with the animate command. The
tcl script would be something like

mol load psf yourpsf.psf

animate read dcd yourdcd.dcd beg 0 end -1 skip 0 waitfor top

set $sel [atomselect top "your selection"]

animate write dcd newfilename.dcd beg 0 end -1 skip 0 selection sell $sel
waitfor top

That should do it! Adjust the beginning/ending frames, and skip if you
like. Check out the documentation here:

Hope that helps,
 On Mar 18, 2014 6:50 AM, "Ramin Ekhteiari" <> wrote:

> Hi ,
> I have a big dcd file, so I would like to remove the water molecules from
> my dcd file and create a new one by using catdcd, but I think I should
> create a index file first to do such a thing,.
> would you please advise me on how to do this.
> Would be grateful for any advice.
> Cheers,
> Ramin.