From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Nov 14 2013 - 06:34:46 CST
Does this mean that you can see the water coords actually but they didn't
change? If so, make sure they were not fixed accidentally, too.
Norman Geist.
Von: Mihaela Drenscko [mailto:quo.physics_at_gmail.com]
Gesendet: Donnerstag, 14. November 2013 11:53
An: Norman Geist
Betreff: Re: namd-l: Separate water coordinates from graphite
Yes, loading the psf and dcd files showed the water on graphite. I used a
script to extract information from dcd file into a Excel file and I saw the
same coordinates (of fixed carbon atoms) and nothing for water, which was
supposed to spread.
Mihaela
On Thu, Nov 14, 2013 at 2:26 AM, Norman Geist
<norman.geist_at_uni-greifswald.de> wrote:
Doesn't the xst only contain the box info? And how can you see what atoms
are inside a DCD, its binary?! Are you sure that you did the simulation with
water inside the box? If so, loading the psf and dcd should show you. Sorry,
but I do not really understand what you're trying to do. Please explain in
more detail.
Norman Geist.
Von: Mihaela Drenscko [mailto:quo.physics_at_gmail.com]
Gesendet: Mittwoch, 13. November 2013 21:14
An: Norman Geist
Betreff: Re: namd-l: Separate water coordinates from graphite
>From dcd or xst file. The problem is that in these files I only saw the
coordinates of fixed carbon atoms, and no water atoms. What could have
caused the absence of water atoms?
Thank you,
Mihaela
On Wed, Nov 13, 2013 at 5:58 AM, Norman Geist
<norman.geist_at_uni-greifswald.de> wrote:
Get the coordinates in which context? From script to process them or written
to a pdb file? For a pdb select your molecule in "VMD Main" window and use
File->Save Coordinates with selection "water". In script, use something
like:
set sel [atomselect top "water"]
$sel get {x y z}
Norman Geist.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Mihaela Drenscko
Gesendet: Dienstag, 12. November 2013 20:57
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: Separate water coordinates from graphite
Hello,
I run a simulation of water on graphite. After simulation, how do I get
water coordinates only, separate from graphite?
Thank you,
Mihaela
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