VMD-L Mailing List
From: Adam Goler (adamgoler_at_gmail.com)
Date: Tue Mar 18 2014 - 09:09:38 CDT
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
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" <ramin_ekh_at_yahoo.com> 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.