AW: Separate water coordinates from graphite

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Nov 14 2013 - 01:26:31 CST

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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